SAXSdb — 2ds5

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

ATP-dependent Clp protease ATP-binding subunit clpX

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–51 Chain B； UniProt 1–51	Fragment：Zinc binding domain(ZBD)	ZN ZINC ION × 2 CA CALCIUM ION × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；100mM Hepes-NaOH, pH 7.5, 200mM calcium chloride, 30% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.50 Å R-free 0.221

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 2DS5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OVX NMR structure of the E. coli ClpX chaperone zinc binding domain dimer Deposited 2003-03-27	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–60（60 aa） Fragment：N-terminal domain (residues 1-60) Chain B 1–60（60 aa） Fragment：N-terminal domain (residues 1-60)	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7.5；303 K；Ionic strength (raw mmCIF value) 150 mM NaCl；Pressure ambient NMR sample composition 1.3 mM ClpX U-15N,13C \| 20 mM sodium phosphate buffer, 0.03% sodium azide, pH 7.5; 150 mM sodium chloride; 90% H2O, 10% H2O	Resolution not provided
2DS6 Structure of the ZBD in the tetragonal crystal form Deposited 2006-06-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–51（51 aa） Fragment：Zinc binding domain(ZBD) Chain B 1–51（51 aa） Fragment：Zinc binding domain(ZBD)	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；100mM tri-sodium citrate, pH 5.6, 2% ethyleneimine polymer, 500mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.313
2DS7 Structure of the ZBD in the hexagonal crystal form Deposited 2006-06-22	Different construct 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 1–51（51 aa） Fragment：Zinc binding domain(ZBD)	Mutation：C43M Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；295 K；100mM sodium acetate, pH 4.6, 200mM lithium sulfate, 12% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.50 Å R-free 0.272
2DS8 Structure of the ZBD-XB complex Deposited 2006-06-22	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 1–51（51 aa） Fragment：Zinc binding domain(ZBD) Chain B 1–51（51 aa） Fragment：Zinc binding domain(ZBD)	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；1.6M tri-sodium citrate, pH 6.5, 10-fold molar excess of XB peptide addition, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.60 Å R-free 0.226
3HTE Crystal structure of nucleotide-free hexameric ClpX Deposited 2009-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 62–424（363 aa） Fragment：Covalently linked ClpX residues 62-424 Chain B 62–424（363 aa） Fragment：Covalently linked ClpX residues 62-424 Chain C 62–424（363 aa） Fragment：Covalently linked ClpX residues 62-424 Chain D 62–424（363 aa） Fragment：Covalently linked ClpX residues 62-424 Chain E 62–424（363 aa） Fragment：Covalently linked ClpX residues 62-424 Chain F 62–424（363 aa） Fragment：Covalently linked ClpX residues 62-424	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；75 mM Sodium acetate, 1.9 M ammonium sulfate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 4.03 Å R-free 0.313
3HWS Crystal structure of nucleotide-bound hexameric ClpX Deposited 2009-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain B 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain C 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain D 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain E 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain F 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain	Mutation：E185Q, K408E Mutation：E185Q, K408E Mutation：E185Q, K408E Mutation：E185Q, K408E Mutation：E185Q, K408E Mutation：E185Q, K408E	ADP ADENOSINE-5'-DIPHOSPHATE × 4 SO4 SULFATE ION × 13 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；Sodium acetate, ammonium sulfate Soaked overnight in mother liquor plus 5 mM ATP-G-S / 5 mM magnesium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.25 Å R-free 0.282
3HWS Crystal structure of nucleotide-bound hexameric ClpX Deposited 2009-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain E 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain F 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain	Mutation：E185Q, K408E Mutation：E185Q, K408E Mutation：E185Q, K408E	ADP ADENOSINE-5'-DIPHOSPHATE × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；Sodium acetate, ammonium sulfate Soaked overnight in mother liquor plus 5 mM ATP-G-S / 5 mM magnesium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.25 Å R-free 0.282
3HWS Crystal structure of nucleotide-bound hexameric ClpX Deposited 2009-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain C 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain Chain D 62–424（363 aa） Fragment：covalently linked ClpX lacking N-terminal domain	Mutation：E185Q, K408E Mutation：E185Q, K408E Mutation：E185Q, K408E	ADP ADENOSINE-5'-DIPHOSPHATE × 2 SO4 SULFATE ION × 9 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；Sodium acetate, ammonium sulfate Soaked overnight in mother liquor plus 5 mM ATP-G-S / 5 mM magnesium chloride, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.25 Å R-free 0.282
4I34 Crystal Structure of W-W-W ClpX Hexamer Deposited 2012-11-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 62–424（363 aa） Chain B 62–424（363 aa） Chain C 62–424（363 aa） Chain D 62–424（363 aa） Chain E 62–424（363 aa） Chain F 62–424（363 aa）	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.8；298 K；75 mM sodium acetate, 1.9 M ammonium sulfate, pH 4.8, VAPOR DIFFUSION, temperature 298K	Resolution 4.12 Å R-free 0.308
4I4L Crystal Structure of Nucleotide-Bound W-W-W ClpX Hexamer Deposited 2012-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 62–424（363 aa） Chain B 62–424（363 aa） Chain C 62–424（363 aa） Chain D 62–424（363 aa） Chain E 62–424（363 aa） Chain F 62–424（363 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.8；298 K；75 mM sodium acetate, 1.9 M ammonium sulfate, pH 4.8, VAPOR DIFFUSION, temperature 298K	Resolution 3.70 Å R-free 0.323
4I5O Crystal Structure of W-W-R ClpX Hexamer Deposited 2012-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 62–424（363 aa） Chain B 62–424（363 aa） Chain C 62–424（363 aa） Chain D 62–424（363 aa） Chain E 62–424（363 aa） Chain F 62–424（363 aa）	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9；298 K；2.2 M ammonium sulfate, 0.2 M ammonium bromide, 0.1 M Bicine, pH 9.0, VAPOR DIFFUSION, temperature 298K	Resolution 4.48 Å R-free 0.323
4I63 Crystal Structure of E-R ClpX Hexamer Deposited 2012-11-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 62–424（363 aa） Chain B 62–424（363 aa） Chain C 62–424（363 aa） Chain D 62–424（363 aa） Chain E 62–424（363 aa） Chain F 62–424（363 aa）	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9；298 K；2.2 M ammonium sulfate, 0.2 M ammonium bromide, 0.1 M bicine, pH 9.0, VAPOR DIFFUSION, temperature 298K	Resolution 5.71 Å R-free 0.315
4I81 Crystal Structure of ATPgS bound ClpX Hexamer Deposited 2012-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 62–424（363 aa） Chain B 62–424（363 aa） Chain C 62–424（363 aa） Chain D 62–424（363 aa） Chain E 62–424（363 aa） Chain F 62–424（363 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.8；298 K；75 mM sodium acetate, 1.9 M ammonium sulfate, pH 4.8, VAPOR DIFFUSION, temperature 298K	Resolution 3.82 Å R-free 0.295
4I9K Crystal structure of symmetric W-W-W ClpX Hexamer Deposited 2012-12-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 62–424（363 aa） Chain B 62–424（363 aa）	Not recorded	SO4 SULFATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；2 M ammonium sulfate, 0.15 M potassium sulfate, 4 mM ATP, 4 mM magnesium sulfate, 50 mM EDTA, pH 7.5, VAPOR DIFFUSION, temperature 298K	Resolution 5.00 Å R-free 0.354
6WR2 ClpP and ClpX IGF loop in ClpX-ClpP complex bound to ssrA tagged GFP Deposited 2020-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain A 62–424（363 aa） Chain B 62–424（363 aa） Chain C 62–424（363 aa） Chain D 62–424（363 aa） Chain E 62–424（363 aa） Chain F 62–424（363 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.88 Å
6WRF ClpX-ClpP complex bound to GFP-ssrA, recognition complex Deposited 2020-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 62–424（363 aa） Chain B 62–424（363 aa） Chain C 62–424（363 aa） Chain D 62–424（363 aa） Chain E 62–424（363 aa） Chain F 62–424（363 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å
6WSG ClpX-ClpP complex bound to ssrA-tagged GFP, intermediate complex Deposited 2020-04-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 62–424（363 aa） Fragment：UNP residues 62-424 Chain B 62–424（363 aa） Fragment：UNP residues 62-424 Chain C 62–424（363 aa） Fragment：UNP residues 62-424 Chain D 62–424（363 aa） Fragment：UNP residues 62-424 Chain E 62–424（363 aa） Fragment：UNP residues 62-424 Chain F 62–424（363 aa） Fragment：UNP residues 62-424	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
8E7V Cryo-EM structure of substrate-free DNClpX.ClpP from singly capped particles Deposited 2022-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain A 62–424（363 aa） Fragment：UNP residues 62-424 Chain B 62–424（363 aa） Fragment：UNP residues 62-424 Chain C 62–424（363 aa） Fragment：UNP residues 62-424 Chain D 62–424（363 aa） Fragment：UNP residues 62-424 Chain E 62–424（363 aa） Fragment：UNP residues 62-424 Chain F 62–424（363 aa） Fragment：UNP residues 62-424	Mutation：C169S, K408E Mutation：C169S, K408E Mutation：C169S, K408E Mutation：C169S, K408E Mutation：C169S, K408E Mutation：C169S, K408E	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8E8Q Cryo-EM structure of substrate-free DNClpX.ClpP Deposited 2022-08-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain A 62–424（363 aa） Fragment：UNP residues 62-424 Chain B 62–424（363 aa） Fragment：UNP residues 62-424 Chain C 62–424（363 aa） Fragment：UNP residues 62-424 Chain D 62–424（363 aa） Fragment：UNP residues 62-424 Chain E 62–424（363 aa） Fragment：UNP residues 62-424 Chain F 62–424（363 aa） Fragment：UNP residues 62-424	Mutation：C169S, K408E Mutation：C169S, K408E Mutation：C169S, K408E Mutation：C169S, K408E Mutation：C169S, K408E Mutation：C169S, K408E	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.12 Å
8V9R Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Poised to Unfold a Branched-Degron DHFR-ssrA Substrate Bound with MTX Deposited 2023-12-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain A 62–424（363 aa） Fragment：UNP residues 62-424 Chain B 62–424（363 aa） Fragment：UNP residues 62-424 Chain C 62–424（363 aa） Fragment：UNP residues 62-424 Chain D 62–424（363 aa） Fragment：UNP residues 62-424 Chain E 62–424（363 aa） Fragment：UNP residues 62-424 Chain F 62–424（363 aa） Fragment：UNP residues 62-424	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MTX METHOTREXATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9C87 Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Poised to Unfold a Linear-Degron DHFR-ssrA Substrate Bound with MTX Deposited 2024-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain A 62–424（363 aa） Chain B 62–424（363 aa） Chain C 62–424（363 aa） Chain D 62–424（363 aa） Chain E 62–424（363 aa） Chain F 62–424（363 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3 MTX METHOTREXATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9C88 Cryo-EM Structure of a Proteolytic ClpXP AAA+ Machine Translocating a Portion of a Branched-Degron DHFR Substrate Deposited 2024-06-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric	Chain A 62–424（363 aa） Fragment：UNP residues 62-424 Chain B 62–424（363 aa） Fragment：UNP residues 62-424 Chain C 62–424（363 aa） Fragment：UNP residues 62-424 Chain D 62–424（363 aa） Fragment：UNP residues 62-424 Chain E 62–424（363 aa） Fragment：UNP residues 62-424 Chain F 62–424（363 aa） Fragment：UNP residues 62-424	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å

20 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CLPX_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–51； UniProt 1–51 Author chain B； PDBConstruct 1–51； UniProt 1–51

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2ds5
Deposition date deposition_date	2006-06-22
Structure title title	Structure of the ZBD in the orthorhomibic crystal from
Keywords keywords	treble cleft zinc finger, METAL BINDING PROTEIN, PROTEIN BINDING; METAL BINDING PROTEIN, PROTEIN BINDING
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	14.08 Å
Radius of gyration Rg (electron density) rg_electron	13.06 Å
Forward intensity I(0) i0	2335160.00
Molecular weight molecular_weight	10081.0 kDa
Excluded volume excluded_volume	12430 Å³
Envelope volume envelope_volume	14441 Å³
Hydration-shell volume shell_volume	9720 Å³
Envelope diameter envelope_diameter	46.0 Å
Shell Rg shell_rg	18.16 Å
Envelope Rg envelope_rg	13.70 Å
Shape Rg shape_rg	13.10 Å
Total Rg total_rg	14.12 Å
Total atoms total_atoms	690
Residues n_residues	87
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	46.8 Å
Rg (real space) rg_real	14.05 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	2.3350e+06
I(0) uncertainty (real space) i0_real_error	2.9870e+04
Rg (reciprocal space) rg_reciprocal	14.05 Å
I(0) (reciprocal space) i0_reciprocal	2335000.0000
Solution quality estimate total_estimate	0.8779
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.2 Å
Skewness Skewness skewness	0.278
Kurtosis Kurtosis kurtosis	-0.227
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	308300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.839; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.905

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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	ATP-dependent Clp protease ATP-binding subunit clpX
Molecular weight formula_weight	5758.6 kDa
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	815

TDKRKDGSGKLLYCSFCGKSQHEVRKLIAGPSVYICDECVDLCNDIIREEI

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	125

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2ds5a_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.11 — ClpX chaperone zinc binding domain

Domain ID domain_id	d2ds5b_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.11 — ClpX chaperone zinc binding domain

CATH v4.4 (2 domains)

Domain ID domain_id	2ds5A00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	220 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — ClpX chaperone, C4-type zinc finger domain

Domain ID domain_id	2ds5B00
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	220 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — ClpX chaperone, C4-type zinc finger domain

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8. Citations (1)

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Unit-cell length a length_a	32.523 Å
Unit-cell length b length_b	43.399 Å
Unit-cell length c length_c	67.719 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1890
R_work r_work	0.1850
R_free r_free	0.2210

fit	/app/data/saxs_computation/ds/2ds5/2ds5.fit
pddf	/app/data/pr_computation/ds/2ds5/2ds5.pr.out
profile	/app/data/saxs_computation/ds/2ds5/2ds5.dat

Structure of the ZBD in the orthorhomibic crystal from

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

ATP-dependent Clp protease ATP-binding subunit clpX

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