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3asw

Structural and biochemical characterization of ClfB:ligand interactions

Method: X-RAY DIFFRACTION Dmax: 85.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Clumping factor B

Staphylococcus aureus

UniProt Q7A382

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 212–531 Fragment：N2 N3 domain (UNP RESIDUES 212-531) Mutation：D444E Tail region derived peptide × 1 （P13645） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；298 K；0.9M sodium citrate, 90mM imidazole pH 8.0 , VAPOR DIFFUSION, temperature 298K Resolution 2.60 Å R-free 0.219

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 3ASW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3AT0 Structural and biochemical characterization of ClfB:ligand interactions Deposited 2010-12-23 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 212–541（330 aa） Fragment：N2 N3 domain (UNP RESIDUES 212-541)
Mutation：D444E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；0.9M sodium citrate, 90mM imidazole pH 8.0, VAPOR DIFFUSION, temperature 298K
Resolution 2.50 Å R-free 0.207
3AU0 Structural and biochemical characterization of ClfB:ligand interactions Deposited 2011-01-28 Different construct 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 203–541（339 aa） Fragment：N2 and N3 domain (UNP RESIDUES 203-541)
Mutation：D444E MG MAGNESIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.7M sodium formate, 1.44M sodium citrate, VAPOR DIFFUSION, temperature 293K
Resolution 2.45 Å R-free 0.279

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CLFB_STAAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 9–328； UniProt 212–531

Tail region derived peptide

OrganismNot specified

UniProt P13645

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 473–487 Not recorded Clumping factor B × 1 （Q7A382） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；298 K；0.9M sodium citrate, 90mM imidazole pH 8.0 , VAPOR DIFFUSION, temperature 298K Resolution 2.60 Å R-free 0.219

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 3ASW Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4F1Z Crystal structures reveal the multi-ligand binding mechanism of the Staphylococcus aureus ClfB Deposited 2012-05-07 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Q 473–486（14 aa） Fragment：tail region, UNP residues 473-486
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；0.1M sodium citrate tribasic dehydrate, 20% 2-propanol, 20% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.30 Å R-free 0.251
4ZRY Crystal structure of the heterocomplex between coil 2B domains of human intermediate filament proteins keratin 1 (KRT1) and keratin 10 (KRT10) Deposited 2015-05-12 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 337–456（120 aa） Fragment：coil 2B domain (UNP residues 337-456)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298.15 K；0.1 M HEPES, 2.0 M ammonium formate
Resolution 3.30 Å R-free 0.277
4ZRY Crystal structure of the heterocomplex between coil 2B domains of human intermediate filament proteins keratin 1 (KRT1) and keratin 10 (KRT10) Deposited 2015-05-12 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 337–456（120 aa） Fragment：coil 2B domain (UNP residues 337-456)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298.15 K；0.1 M HEPES, 2.0 M ammonium formate
Resolution 3.30 Å R-free 0.277
6E2J Crystal structure of the heterocomplex between human keratin 1 coil 1B containing S233L mutation and wild-type human keratin 10 coil 1B Deposited 2018-07-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 195–296（102 aa）
Not recorded SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.1 M Tris, 1.5 M ammonium sulfate, 12% glycerol
Resolution 2.39 Å R-free 0.294
6E2J Crystal structure of the heterocomplex between human keratin 1 coil 1B containing S233L mutation and wild-type human keratin 10 coil 1B Deposited 2018-07-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 195–296（102 aa）
Not recorded SO4 SULFATE ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.1 M Tris, 1.5 M ammonium sulfate, 12% glycerol
Resolution 2.39 Å R-free 0.294
6EC0 Crystal structure of the wild-type heterocomplex between coil 1B domains of human intermediate filament proteins keratin 1 (KRT1) and keratin 10 (KRT10) Deposited 2018-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 195–296（102 aa）
Not recorded CD CADMIUM ION × 8 CO COBALT (II) ION × 4 NI NICKEL (II) ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；11% PEG 3350, 0.1 M HEPES, 5 mM cobalt chloride, 5 mM cadmium chloride, 5 mM magnesium chloride, 5 mM nickel chloride
Resolution 2.98 Å R-free 0.300
6UUI Crystal structure of the heterocomplex between coil 2B domains of wild-type keratin 1 (KRT1) and keratin 10 (KRT10) containing mutation Cys401Ala Deposited 2019-10-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain X 337–456（120 aa） Fragment：2B domain
Mutation：C401A BOG octyl beta-D-glucopyranoside × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；285.15 K；Ammonium phosphate dibasic, Tris, N-octyl-B-D-glucoside
Resolution 2.07 Å R-free 0.277

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name K1C10_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–15； UniProt 473–487

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 3asw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3asw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3asw
Deposition date deposition_date2010-12-22
Structure title titleStructural and biochemical characterization of ClfB:ligand interactions
Keywords keywordsIgG like, Adhesin, Cytokeratin, CELL ADHESION; CELL ADHESION
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_guinier23.30 Å
Radius of gyration Rg (electron density) rg_electron22.76 Å
Forward intensity I(0) i023108100.00
Molecular weight molecular_weight35623.0 kDa
Excluded volume excluded_volume44012 ų
Envelope volume envelope_volume52424 ų
Hydration-shell volume shell_volume20479 ų
Envelope diameter envelope_diameter87.2 Å
Shell Rg shell_rg28.39 Å
Envelope Rg envelope_rg23.07 Å
Shape Rg shape_rg22.75 Å
Total Rg total_rg23.47 Å
Total atoms total_atoms2519
Residues n_residues331
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 dmax85.0 Å
Rg (real space) rg_real23.50 Å
Rg uncertainty (real space) rg_real_error0.72 Å
I(0) (real space) i0_real2.3110e+07
I(0) uncertainty (real space) i0_real_error3.5850e+05
Rg (reciprocal space) rg_reciprocal23.45 Å
I(0) (reciprocal space) i0_reciprocal23110000.0000
Solution quality estimate total_estimate0.8085
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.5 Å
Skewness Skewness skewness0.606
Kurtosis Kurtosis kurtosis-0.001
Angular range angular_range— – 0.3400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4163000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.617; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.746; Smooth: 0.909
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3aswA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1280 —
Domain ID domain_id3aswA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1290 —
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8. Citations (1)

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9. Files and Curves (10)