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4mjp

E. coli sliding clamp in complex with (R)-Vedaprofen

Method: X-RAY DIFFRACTION Dmax: 97.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase III subunit beta

Escherichia coli

UniProt P0A988

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–366 Chain B； UniProt 1–366 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

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 4MJP 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 oligomeric state 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 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 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 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 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 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
3D1F Crystal structure of E. coli sliding clamp (beta) bound to a polymerase III peptide Deposited 2008-05-05 Different oligomeric state 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 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
3D1G Structure of a small molecule inhibitor bound to a DNA sliding clamp Deposited 2008-05-05 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 ligand/ion 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 ligand/ion 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 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 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 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 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 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 ligand/ion 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
4MJQ E. coli sliding clamp in complex with Bromfenac Deposited 2013-09-04 Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 ligand/ion 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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

SAXS profile for 4mjp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4mjp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4mjp
Deposition date deposition_date2013-09-04
Structure title titleE. coli sliding clamp in complex with (R)-Vedaprofen
Keywords keywordsPolIII beta, sliding clamp, DnaN, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.00 Å
Radius of gyration Rg (electron density) rg_electron31.86 Å
Forward intensity I(0) i0103724000.00
Molecular weight molecular_weight80225.0 kDa
Excluded volume excluded_volume100300 ų
Envelope volume envelope_volume138570 ų
Hydration-shell volume shell_volume35471 ų
Envelope diameter envelope_diameter95.2 Å
Shell Rg shell_rg40.16 Å
Envelope Rg envelope_rg30.40 Å
Shape Rg shape_rg31.88 Å
Total Rg total_rg32.53 Å
Total atoms total_atoms5617
Residues n_residues720
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax97.2 Å
Rg (real space) rg_real32.79 Å
Rg uncertainty (real space) rg_real_error0.62 Å
I(0) (real space) i0_real1.0370e+08
I(0) uncertainty (real space) i0_real_error1.6190e+06
Rg (reciprocal space) rg_reciprocal32.89 Å
I(0) (reciprocal space) i0_reciprocal103700000.0000
Solution quality estimate total_estimate0.9008
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.6 Å
Skewness Skewness skewness-0.038
Kurtosis Kurtosis kurtosis-0.852
Angular range angular_range— – 0.2400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha81310000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.947
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd4mjpa1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.131 — DNA clamp
Superfamily Superfamily superfamilyd.131.1 — DNA clamp
Family Family familyd.131.1.1 — DNA polymerase III, beta subunit
Domain ID domain_idd4mjpa2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.131 — DNA clamp
Superfamily Superfamily superfamilyd.131.1 — DNA clamp
Family Family familyd.131.1.1 — DNA polymerase III, beta subunit
Domain ID domain_idd4mjpa3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.131 — DNA clamp
Superfamily Superfamily superfamilyd.131.1 — DNA clamp
Family Family familyd.131.1.1 — DNA polymerase III, beta subunit
Domain ID domain_idd4mjpb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.131 — DNA clamp
Superfamily Superfamily superfamilyd.131.1 — DNA clamp
Family Family familyd.131.1.1 — DNA polymerase III, beta subunit
Domain ID domain_idd4mjpb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.131 — DNA clamp
Superfamily Superfamily superfamilyd.131.1 — DNA clamp
Family Family familyd.131.1.1 — DNA polymerase III, beta subunit
Domain ID domain_idd4mjpb3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.131 — DNA clamp
Superfamily Superfamily superfamilyd.131.1 — DNA clamp
Family Family familyd.131.1.1 — DNA polymerase III, beta subunit

CATH v4.4 (6 domains)

Domain ID domain_id4mjpA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily10 — DNA Polymerase III, subunit A, domain 2
Domain ID domain_id4mjpA02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily10 — DNA Polymerase III, subunit A, domain 2
Domain ID domain_id4mjpA03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily10 — DNA Polymerase III, subunit A, domain 2
Domain ID domain_id4mjpB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily10 — DNA Polymerase III, subunit A, domain 2
Domain ID domain_id4mjpB02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily10 — DNA Polymerase III, subunit A, domain 2
Domain ID domain_id4mjpB03
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology150 — DNA Polymerase III; Chain A, domain 2
Homologous superfamily homologous superfamily10 — DNA Polymerase III, subunit A, domain 2
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8. Citations (1)

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9. Files and Curves (10)