3d1f

Crystal structure of E. coli sliding clamp (beta) bound to a polymerase III peptide

Method: X-RAY DIFFRACTION D_max: 98.6 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase III subunit beta

Escherichia coli

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–366 Chain B； UniProt 1–366	Not recorded	Nonapeptide from polymerase III C-terminal × 2 PEG DI(HYDROXYETHYL)ETHER × 2 323 2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.2；295 K；27.5% PEG400, 100 mM MES pH 6.2, 100 mM calcium chloride and 1% DMSO, VAPOR DIFFUSION, temperature 295K	Resolution 2.00 Å R-free 0.255

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3D1F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JQJ Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader Complex of E. coli DNA Polymerase III: Structure of the beta-delta complex Deposited 2001-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa）	Mutation：I272A, L273A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；TRIS, Ammonium phosphate, dithiothreitol, ammonium tartartate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K	Resolution 2.90 Å R-free 0.308
1JQJ Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader Complex of E. coli DNA Polymerase III: Structure of the beta-delta complex Deposited 2001-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–366（366 aa）	Mutation：I272A, L273A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；TRIS, Ammonium phosphate, dithiothreitol, ammonium tartartate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K	Resolution 2.90 Å R-free 0.308
1JQJ Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader Complex of E. coli DNA Polymerase III: Structure of the beta-delta complex Deposited 2001-08-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Mutation：I272A, L273A Mutation：I272A, L273A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；TRIS, Ammonium phosphate, dithiothreitol, ammonium tartartate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K	Resolution 2.90 Å R-free 0.308
1JQJ Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader Complex of E. coli DNA Polymerase III: Structure of the beta-delta complex Deposited 2001-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–366（366 aa）	Mutation：I272A, L273A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；TRIS, Ammonium phosphate, dithiothreitol, ammonium tartartate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K	Resolution 2.90 Å R-free 0.308
1JQJ Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader Complex of E. coli DNA Polymerase III: Structure of the beta-delta complex Deposited 2001-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–366（366 aa）	Mutation：I272A, L273A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；TRIS, Ammonium phosphate, dithiothreitol, ammonium tartartate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 21K	Resolution 2.90 Å R-free 0.308
1JQL Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader Complex of E. coli DNA Polymerase III: Structure of beta-delta (1-140) Deposited 2001-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa）	Mutation：I272A, L273A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；294 K；TRIS-HCL, polyethylene glycol 4000, MgCl2, dithiothreitol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 21K	Resolution 2.50 Å R-free 0.294
1MMI E. COLI DNA POLYMERASE BETA SUBUNIT Deposited 2002-09-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；100 mM Na/H MES, 50 to 60 mM CaCl2, 30% v/v PEG 400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.85 Å R-free 0.245
2POL THREE-DIMENSIONAL STRUCTURE OF THE BETA SUBUNIT OF ESCHERICHIA COLI DNA POLYMERASE III HOLOENZYME: A SLIDING DNA CLAMP Deposited 1992-11-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
2XUR The G157C mutation in the Escherichia coli sliding clamp specifically affects initiation of replication Deposited 2010-10-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Mutation：YES Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.252
3BEP Structure of a sliding clamp on DNA Deposited 2007-11-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	5CY 1-(3-hydroxypropyl)-2-{(1E,3E,5E)-5-[1-(3-hydroxypropyl)-3,3-dimethyl-1,3-dihydro-2H-indol-2-ylidene]penta-1,3-dien-1-y l}-3,3-dimethyl-3H-indolium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.9；298 K；26% PEG 400, 75mM MES (pH 5.9), 75mM CaCl2, 5% glycerol, 0.5% DMSO, VAPOR DIFFUSION, temperature 298K	Resolution 1.92 Å R-free 0.268
3D1E Crystal structure of E. coli sliding clamp (beta) bound to a polymerase II peptide Deposited 2008-05-05	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.2；295 K；27.5% PEG400, 100 mM MES pH 6.2, 100 mM calcium chloride and 1% DMSO, VAPOR DIFFUSION, temperature 295K	Resolution 1.90 Å R-free 0.261
3D1G Structure of a small molecule inhibitor bound to a DNA sliding clamp Deposited 2008-05-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	322 [(5R)-5-(2,3-dibromo-5-ethoxy-4-hydroxybenzyl)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.1；295 K；25% PEG400, 100 mM MES pH 6.1, 100 mM calcium chloride, and 3% DMSO, VAPOR DIFFUSION, temperature 295K	Resolution 1.64 Å R-free 0.296
3F1V E. coli Beta Sliding Clamp, 148-153 Ala Mutant Deposited 2008-10-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Mutation：H148A, Q149A, D150A, V151A, R152A Mutation：H148A, Q149A, D150A, V151A, R152A	CA CALCIUM ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；reservior: 13% isopropanol, 100 mM CaCl2, 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.77 Å R-free 0.282
3PWE Crystal structure of the E. coli beta clamp mutant R103C, I305C, C260S, C333S at 2.2A resolution Deposited 2010-12-08	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Mutation：R103C, I305C, C260S, C333S Mutation：R103C, I305C, C260S, C333S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；296 K；100 mM MES pH 6.0, 125 mM calcium chloride, 30% PEG 400 added in a 1:1 ratio to 1.8 mg/mL protein solution, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.20 Å R-free 0.245
3Q4J Structure of a small peptide ligand bound to E.coli DNA sliding clamp Deposited 2010-12-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–366（366 aa） Chain D 1–366（366 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；0.1 M MES PH 6.0, 0.1M CaCl2, 30% PEG 400, vapor diffusion, temperature 298K	Resolution 2.30 Å R-free 0.254
3Q4J Structure of a small peptide ligand bound to E.coli DNA sliding clamp Deposited 2010-12-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–366（366 aa） Chain F 1–366（366 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；0.1 M MES PH 6.0, 0.1M CaCl2, 30% PEG 400, vapor diffusion, temperature 298K	Resolution 2.30 Å R-free 0.254
3Q4J Structure of a small peptide ligand bound to E.coli DNA sliding clamp Deposited 2010-12-23	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；0.1 M MES PH 6.0, 0.1M CaCl2, 30% PEG 400, vapor diffusion, temperature 298K	Resolution 2.30 Å R-free 0.254
3Q4K Structure of a small peptide ligand bound to E.coli DNA sliding clamp Deposited 2010-12-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；0.1 M MES PH 6.0, 0.1M CaCl2, 30% PEG 400 + 0.2% agarose in drop, temperature 298K, VAPOR DIFFUSION	Resolution 2.60 Å R-free 0.294
3Q4L Structure of a small peptide ligand bound to E.coli DNA sliding clamp Deposited 2010-12-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；298 K；0.1 M MES PH 6.0, 0.1M CaCl2, 30% PEG 400, vapor diffusion, temperature 298K	Resolution 1.95 Å R-free 0.232
3QSB Structure of E. coli polIIIbeta with (Z)-5-(1-((4'-Fluorobiphenyl-4-yl)methoxyimino)butyl)-2,2-dimethyl-4,6-dioxocyclohexanecarbonitrile Deposited 2011-02-20	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	743 (1R,5R)-5-{(1Z)-N-[(4'-fluorobiphenyl-4-yl)methoxy]butanimidoyl}-2,2-dimethyl-4,6-dioxocyclohexanecarbonitrile × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；100mM Na MES pH 6.0, 50-60mM CaCl2, 30%(v/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.90 Å R-free 0.317
4K3K E. Coli sliding clamp in complex with (S)-2-(4-methylpentanamido)-3-phenylpropanoic acid Deposited 2013-04-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	CA CALCIUM ION × 4 PG4 TETRAETHYLENE GLYCOL × 4 PEG DI(HYDROXYETHYL)ETHER × 1 SFK N-(4-methylpentanoyl)-L-phenylalanine × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.85 Å R-free 0.230
4K3L E. coli sliding clamp in complex with AcLF dipeptide Deposited 2013-04-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	LEU LEUCINE × 2 PHE PHENYLALANINE × 2 CA CALCIUM ION × 12 PEG DI(HYDROXYETHYL)ETHER × 5 ACE ACETYL GROUP × 2 PGE TRIETHYLENE GLYCOL × 1 EDO 1,2-ETHANEDIOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.50 Å R-free 0.255
4K3M E.coli sliding clamp in complex with AcALDLF peptide Deposited 2013-04-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 3 CA CALCIUM ION × 7 PGE TRIETHYLENE GLYCOL × 2 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.85 Å R-free 0.258
4K3O E. coli sliding clamp in complex with AcQADLF Deposited 2013-04-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 4 CA CALCIUM ION × 8 PGE TRIETHYLENE GLYCOL × 3 EDO 1,2-ETHANEDIOL × 2 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 2.00 Å R-free 0.248
4K3P E. coli sliding clamp in complex with AcQLALF Deposited 2013-04-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	CA CALCIUM ION × 5 EDO 1,2-ETHANEDIOL × 1 PG4 TETRAETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 2.15 Å R-free 0.273
4K3Q E. coli sliding clamp in complex with AcQLDAF Deposited 2013-04-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 6 CA CALCIUM ION × 7 PGE TRIETHYLENE GLYCOL × 3 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.85 Å R-free 0.242
4K3R E. coli sliding clamp in complex with AcQLDLA Deposited 2013-04-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 3 CA CALCIUM ION × 2 PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.86 Å R-free 0.264
4K3S E. coli sliding clamp in P1 crystal space group Deposited 2013-04-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	CA CALCIUM ION × 1 PG4 TETRAETHYLENE GLYCOL × 1 P4C O-ACETALDEHYDYL-HEXAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.75 Å R-free 0.229
4MJP E. coli sliding clamp in complex with (R)-Vedaprofen Deposited 2013-09-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 2 CA CALCIUM ION × 1 CL CHLORIDE ION × 3 27O (2R)-2-(4-cyclohexylnaphthalen-1-yl)propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.85 Å R-free 0.237
4MJQ E. coli sliding clamp in complex with Bromfenac Deposited 2013-09-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	27R [2-amino-3-(4-bromobenzoyl)phenyl]acetic acid × 1 PGE TRIETHYLENE GLYCOL × 2 CA CALCIUM ION × 3 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.73 Å R-free 0.218
4MJR E. coli sliding clamp in complex with (S)-Carprofen Deposited 2013-09-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	PGE TRIETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 4 CL CHLORIDE ION × 3 0LA (2S)-2-(6-chloro-9H-carbazol-2-yl)propanoic acid × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.62 Å R-free 0.225
4N94 E. coli sliding clamp in complex with 3,4-difluorobenzamide Deposited 2013-10-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	2HO 3,4-difluorobenzamide × 1 CL CHLORIDE ION × 1 PG4 TETRAETHYLENE GLYCOL × 2 CA CALCIUM ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.73 Å R-free 0.293
4N95 E. coli sliding clamp in complex with 5-chloroindoline-2,3-dione Deposited 2013-10-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 5 2HQ 5-chloro-1H-indole-2,3-dione × 1 CL CHLORIDE ION × 1 PGE TRIETHYLENE GLYCOL × 1 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.80 Å R-free 0.224
4N96 E. coli sliding clamp in complex with 6-nitroindazole Deposited 2013-10-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	6NI 6-NITROINDAZOLE × 1 CA CALCIUM ION × 3 CL CHLORIDE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.70 Å R-free 0.275
4N97 E. coli sliding clamp in complex with 5-nitroindole Deposited 2013-10-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	2HU 5-nitro-1H-indole × 1 PEG DI(HYDROXYETHYL)ETHER × 4 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.97 Å R-free 0.306
4N98 E. coli sliding clamp in complex with 4'-fluorobiphenyl-4-carboxylic acid Deposited 2013-10-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	4FC 4'-FLUORO-1,1'-BIPHENYL-4-CARBOXYLIC ACID × 1 CA CALCIUM ION × 9 PEG DI(HYDROXYETHYL)ETHER × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.70 Å R-free 0.296
4N99 E. coli sliding clamp in complex with 6-chloro-2,3,4,9-tetrahydro-1H-carbazole-7-carboxylic acid Deposited 2013-10-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	2J1 6-chloro-2,3,4,9-tetrahydro-1H-carbazole-7-carboxylic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 19 PG4 TETRAETHYLENE GLYCOL × 10 CA CALCIUM ION × 5	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.338
4N9A E. coli sliding clamp in complex with (R)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxylic acid Deposited 2013-10-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	CA CALCIUM ION × 5 PG4 TETRAETHYLENE GLYCOL × 1 2J2 (1R)-6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxylic acid × 1 PEG DI(HYDROXYETHYL)ETHER × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；285 K；100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 1.90 Å R-free 0.261
5FKU cryo-EM structure of the E. coli replicative DNA polymerase complex in DNA free state (DNA polymerase III alpha, beta, epsilon, tau complex) Deposited 2015-10-20	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–366（366 aa） Chain C 1–366（366 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT；pH 7.5；25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 8.34 Å
5FKV cryo-EM structure of the E. coli replicative DNA polymerase complex bound to DNA (DNA polymerase III alpha, beta, epsilon, tau complex) Deposited 2015-10-20	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain B 1–366（366 aa） Chain C 1–366（366 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT；pH 7.5；25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 8.04 Å
5FKW cryo-EM structure of the E. coli replicative DNA polymerase complex bound to DNA (DNA polymerase III alpha, beta, epsilon) Deposited 2015-10-20	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 1–366（366 aa） Chain C 1–366（366 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT；pH 7.5；25 MM HEPES PH 7.5, 150 MM NACL, AND 2 MM DTT cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 7.30 Å
5M1S Cryo-EM structure of the E. coli replicative DNA polymerase-clamp-exonuclase-theta complex bound to DNA in the editing mode Deposited 2016-10-10	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain B 1–366（366 aa） Chain C 1–366（366 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Prior to sample preparation 0.1 volumes of 0.05% Tween 20 were added to the sample 3 microliters were pipetted onto the grid and blotted for 4 seconds	Resolution 6.70 Å
6E8E Crystal structure of the Escherichia coli sliding clamp-MutL complex. Deposited 2018-07-28	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 6 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100 mM Bis-Tris pH 5.5, 2 M ammonium sulfate.	Resolution 2.25 Å R-free 0.225
6FVL DNA polymerase sliding clamp from Escherichia coli with bound P7 peptide Deposited 2018-03-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	1PE PENTAETHYLENE GLYCOL × 11 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；MES 50mM pH 6, CaCl2 50mM PEG400 30% (1 microliter) + Hampton Research PEG Ion kit E6 (1 microliter): 0.2M sodium malonate pH6, 20% PEG 3350	Resolution 1.98 Å R-free 0.233
6FVL DNA polymerase sliding clamp from Escherichia coli with bound P7 peptide Deposited 2018-03-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–366（366 aa） Chain D 1–366（366 aa）	Not recorded	1PE PENTAETHYLENE GLYCOL × 6 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；MES 50mM pH 6, CaCl2 50mM PEG400 30% (1 microliter) + Hampton Research PEG Ion kit E6 (1 microliter): 0.2M sodium malonate pH6, 20% PEG 3350	Resolution 1.98 Å R-free 0.233
8CIX DNA-polymerase sliding clamp (DnaN) from Escherichia coli in complex with Griselimycin. Deposited 2023-02-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–366（366 aa）	Not recorded	GOL GLYCEROL × 2 CA CALCIUM ION × 14 ACT ACETATE ION × 6 MG MAGNESIUM ION × 8 NA SODIUM ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.7；293 K；0.36 M CaCl2 0.13 M MgCl2 0.24 M Na Acetate 8.3 % (v/v) Glycerol 12.2 % (w/v) PEG 3350 0.1 M HEPES/NaOH 7.7 Cryoprotection: 10 % (v/v) (2R,3R)-2,3-butanediol.	Resolution 1.76 Å R-free 0.205
8CIY DNA-polymerase sliding clamp (DnaN) from Escherichia coli in complex with Cyclohexyl-Griselimycin. Deposited 2023-02-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–366（366 aa）	Not recorded	CA CALCIUM ION × 12 MG MAGNESIUM ION × 10 NA SODIUM ION × 2 GOL GLYCEROL × 4 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.7；293 K；0.64 M CaCl2 0.5 M Li Acetate 9.4 % (w/v) PEG 8000 0.1 M HEPES/NaOH 7.7 Cryoprotection: 10 % (v/v) (2R,3R)-2,3-butanediol	Resolution 1.54 Å R-free 0.200
8CIZ DNA-polymerase sliding clamp (DnaN) from Escherichia coli in complex with Mycoplanecin A. Deposited 2023-02-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–366（366 aa） Chain B 1–366（366 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；0.2 M CaCl2 0.15 M MgCl2 8.75 % (v/v) Glycerol 17.5 % (w/v) PEG 3350 0.1 M Tris/HCl pH 9.0 Cryoprotection: 10 % (v/v) (2R,3R)-2,3-butanediol.	Resolution 2.27 Å R-free 0.237
8GIY E. coli clamp loader with closed clamp Deposited 2023-03-14	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain H 1–366（366 aa） Chain I 1–366（366 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；30 mM Na.HEPES pH 7.5, 3 mM MgCl2, 2 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol, 1 mM ATPgammaS. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8GIZ E. coli clamp loader with open clamp Deposited 2023-03-14	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain H 1–366（366 aa） Chain I 1–366（366 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；30 mM Na.HEPES pH 7.5, 3 mM MgCl2, 2 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol, 1 mM ATPgammaS. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8GJ0 E. coli clamp loader with open clamp on primed template DNA (form 1) Deposited 2023-03-14	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain H 1–366（366 aa） Chain I 1–366（366 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ALF TETRAFLUOROALUMINATE ION × 3 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；30 mM Tris-HCl pH 7.6, 5 mM MgCl2, 2 mM ADP, 0.5 mM AlCl3, 5 mM NaF, 5 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol. cryo-EM vitrification conditions Cryogen ETHANE；3 uL of sample was applied onto a Ultrafoil Au R1.2/1.3 grid. Blot for 4.5 s with no extra force before plunging into liquid ethane.	Resolution 2.90 Å
8GJ1 E. coli clamp loader with open clamp on primed template DNA (form 2) Deposited 2023-03-14	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain H 1–366（366 aa） Chain I 1–366（366 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ALF TETRAFLUOROALUMINATE ION × 3 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；30 mM Tris-HCl pH 7.6, 5 mM MgCl2, 2 mM ADP, 0.5 mM AlCl3, 5 mM NaF, 5 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol. cryo-EM vitrification conditions Cryogen ETHANE；3 uL of sample was applied onto a Ultrafoil Au R1.2/1.3 grid. Blot for 4.5 s with no extra force before plunging into liquid ethane.	Resolution 3.00 Å
8GJ2 E. coli clamp loader with closed clamp on primed template DNA Deposited 2023-03-14	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain H 1–366（366 aa） Chain I 1–366（366 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ALF TETRAFLUOROALUMINATE ION × 3 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；30 mM Tris-HCl pH 7.6, 5 mM MgCl2, 2 mM ADP, 0.5 mM AlCl3, 5 mM NaF, 5 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol. cryo-EM vitrification conditions Cryogen ETHANE；3 uL of sample was applied onto a Ultrafoil Au R1.2/1.3 grid. Blot for 4.5 s with no extra force before plunging into liquid ethane.	Resolution 2.60 Å
8VAL Structure of the E. coli clamp loader bound to the beta clamp in a Open-DNAp/t conformation Deposited 2023-12-11	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8VAM Structure of the E. coli clamp loader bound to the beta clamp in a Semi-Open conformation Deposited 2023-12-11	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8VAP Structure of the E. coli clamp loader bound to the beta clamp in a Fully-Open conformation Deposited 2023-12-11	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8VAQ Structure of the E. coli clamp loader bound to the beta clamp in a Closed-DNA1 conformation Deposited 2023-12-11	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8VAR Structure of the E. coli clamp loader bound to the beta clamp in a Closed-DNA2 conformation Deposited 2023-12-11	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8VAS Structure of the E. coli clamp loader bound to the beta clamp in an Altered-Collar conformation Deposited 2023-12-11	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8VAT Structure of the E. coli clamp loader bound to the beta clamp in a Open-RNAp/t conformation Deposited 2023-12-11	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: nonameric	Chain F 1–366（366 aa） Chain G 1–366（366 aa）	Not recorded	ZN ZINC ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 BEF BERYLLIUM TRIFLUORIDE ION × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

53 other PDB entries and 60 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DPO3B_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–366； UniProt 1–366 Author chain B； PDBConstruct 1–366； UniProt 1–366

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3d1f
Deposition date deposition_date	2008-05-05
Structure title title	Crystal structure of E. coli sliding clamp (beta) bound to a polymerase III peptide
Keywords keywords	;chemical probe, DNA polymerase, DNA sliding clamp, DNA replication, rational drug design, antibiotic target, TRANSFERASE, TRANSCRIPTION ;; TRANSFERASE, TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	33.13 Å
Radius of gyration Rg (electron density) rg_electron	32.03 Å
Forward intensity I(0) i0	114723000.00
Molecular weight molecular_weight	84375.0 kDa
Excluded volume excluded_volume	105450 Å³
Envelope volume envelope_volume	145170 Å³
Hydration-shell volume shell_volume	37007 Å³
Envelope diameter envelope_diameter	97.1 Å
Shell Rg shell_rg	40.31 Å
Envelope Rg envelope_rg	30.61 Å
Shape Rg shape_rg	32.06 Å
Total Rg total_rg	32.65 Å
Total atoms total_atoms	5918
Residues n_residues	750
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	98.6 Å
Rg (real space) rg_real	32.92 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	1.1470e+08
I(0) uncertainty (real space) i0_real_error	1.7220e+06
Rg (reciprocal space) rg_reciprocal	33.02 Å
I(0) (reciprocal space) i0_reciprocal	114700000.0000
Solution quality estimate total_estimate	0.8287
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	49.3 Å
Skewness Skewness skewness	-0.022
Kurtosis Kurtosis kurtosis	-0.835
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	120700000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	DNA polymerase III subunit beta
Molecular weight formula_weight	40630.5 kDa
EC 编号 ec_number	2.7.7.7
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6476

MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYVVMPMRL

来源 Source

来源生物 organism	Escherichia coli
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nonapeptide from polymerase III C-terminal
Molecular weight formula_weight	1095.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q

SEQVELEFD

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-[3,6-bis(dimethylamino)xanthen-9-yl]-5-methanoyl-benzoate
Molecular weight formula_weight	414.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	558

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3d1fa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.1 — DNA polymerase III, beta subunit

Domain ID domain_id	d3d1fa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.1 — DNA polymerase III, beta subunit

Domain ID domain_id	d3d1fa3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.1 — DNA polymerase III, beta subunit

Domain ID domain_id	d3d1fb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.1 — DNA polymerase III, beta subunit

Domain ID domain_id	d3d1fb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.1 — DNA polymerase III, beta subunit

Domain ID domain_id	d3d1fb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.1 — DNA polymerase III, beta subunit

CATH v4.4 (6 domains)

Domain ID domain_id	3d1fA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

Domain ID domain_id	3d1fA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

Domain ID domain_id	3d1fA03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

Domain ID domain_id	3d1fB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

Domain ID domain_id	3d1fB02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

Domain ID domain_id	3d1fB03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — DNA Polymerase III, subunit A, domain 2

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8. Citations (1)

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Unit-cell length a length_a	65.778 Å
Unit-cell length b length_b	65.778 Å
Unit-cell length c length_c	209.472 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	44.140 Å
R factor r_factor	—
R_work r_work	0.2170
R_free r_free	0.2550

fit	/app/data/saxs_computation/d1/3d1f/3d1f.fit
pddf	/app/data/pr_computation/d1/3d1f/3d1f.pr.out
profile	/app/data/saxs_computation/d1/3d1f/3d1f.dat

Crystal structure of E. coli sliding clamp (beta) bound to a polymerase III peptide

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase III subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)