SAXSdb — 2f6a

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

Collagen adhesin

Staphylococcus aureus

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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 30–330 Chain C； UniProt 30–330	Fragment：extracellular domain	Collagen × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.35；295 K；0.8 M ammonium sulfate, 0.5 M sodium acetate, PH 6.5, pH 7.35, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.29 Å R-free 0.308
2	Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain B； UniProt 30–330 Chain D； UniProt 30–330	Fragment：extracellular domain	Collagen × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.35；295 K；0.8 M ammonium sulfate, 0.5 M sodium acetate, PH 6.5, pH 7.35, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.29 Å R-free 0.308
3	Protein heterocomplex Heteromer Protein × 20 PDB declaration: eicosameric（20） Consistent with protein copy count	Chain A； UniProt 30–330 Chain B； UniProt 30–330 Chain C； UniProt 30–330 Chain D； UniProt 30–330	Fragment：extracellular domain	Collagen × 12	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.35；295 K；0.8 M ammonium sulfate, 0.5 M sodium acetate, PH 6.5, pH 7.35, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 3.29 Å R-free 0.308

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 2F6A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AMX COLLAGEN-BINDING DOMAIN FROM A STAPHYLOCOCCUS AUREUS ADHESIN Deposited 1997-06-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 151–318（168 aa） Fragment：CBD (151 - 318)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.7；pH 6.7	Resolution 2.00 Å R-free 0.249
1D2O CRYSTAL STRUCTURE OF A SINGLE B REPEAT UNIT (B1) OF COLLAGEN BINDING SURFACE PROTEIN (CNA) OF STAPHYLOCOCCUS AUREUS. Deposited 1999-09-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 533–719（187 aa） Fragment：SINGLE B REPEAT UNIT Chain B 533–719（187 aa） Fragment：SINGLE B REPEAT UNIT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；Ammonium sulfate, Succinic acid buffer, BOG , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.256
1D2P CRYSTAL STRUCTURE OF TWO B REPEAT UNITS (B1B2) OF THE COLLAGEN BINDING PROTEIN (CNA) OF STAPHYLOCOCCUS AUREUS Deposited 1999-09-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 533–905（373 aa） Fragment：B REPEAT REGIONS	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG6000, Calcium chloride, sodium cacodylate , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.245
2F68 Crystal structure of collagen adhesin (CNA) from S. aureus Deposited 2005-11-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 30–334（305 aa） Fragment：Extracellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；295 K；3.2 M Ammonium Sulfate, 0.1 M NaCl, 0.05 M Hepes, PH. 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.95 Å R-free 0.253

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CNA_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–303； UniProt 30–330 Author chain B； PDBConstruct 3–303； UniProt 30–330 Author chain C； PDBConstruct 3–303； UniProt 30–330 Author chain D； PDBConstruct 3–303； UniProt 30–330

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	2f6a
Deposition date deposition_date	2005-11-28
Structure title title	Collagen Adhesin and Collagen Complex Structure
Keywords keywords	CNA, Collagen, MSCRAMM, Adhesion, ECM, CELL ADHESION-STRUCTURAL PROTEIN COMPLEX; CELL ADHESION/STRUCTURAL PROTEIN
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	41.28 Å
Radius of gyration Rg (electron density) rg_electron	41.21 Å
Forward intensity I(0) i0	352794000.00
Molecular weight molecular_weight	147420.0 kDa
Excluded volume excluded_volume	182330 Å³
Envelope volume envelope_volume	269960 Å³
Hydration-shell volume shell_volume	56988 Å³
Envelope diameter envelope_diameter	153.8 Å
Shell Rg shell_rg	44.28 Å
Envelope Rg envelope_rg	40.95 Å
Shape Rg shape_rg	41.14 Å
Total Rg total_rg	41.61 Å
Total atoms total_atoms	10394
Residues n_residues	1331
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	139.9 Å
Rg (real space) rg_real	41.36 Å
Rg uncertainty (real space) rg_real_error	1.40 Å
I(0) (real space) i0_real	3.5280e+08
I(0) uncertainty (real space) i0_real_error	6.5290e+06
Rg (reciprocal space) rg_reciprocal	41.28 Å
I(0) (reciprocal space) i0_reciprocal	352800000.0000
Solution quality estimate total_estimate	0.8689
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	51.5 Å
Skewness Skewness skewness	0.413
Kurtosis Kurtosis kurtosis	-0.228
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22240000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.865

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Collagen adhesin
Molecular weight formula_weight	33131.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	10394

GSARDISSTNVTDLTVSPSKIEDGGKTTVKMTFDDKNGKIQNGDMIKVAWPTSGTVKIEGYSKTVPLTVKGEQVGQAVITPDGATITFNDKVEKLSDVSGFAEFEVQGRNLTQTNTSDDKVATITSGNKSTNVTVHKSEAGTSSVFYYKTGDMLPEDTTHVRWFLNINNEKSYVSKDITIKDQIQGGQQLDLSTLNINVTGTHSNYYSGQSAITDFEKAFPGSKITVDNTKNTIDVTIPQGYGSYNSFSINYKTKITNEQQKEFVNNSQAWYQEHGKEEVNGKSFNHTVHNINANAGIEGTVK

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI Class编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Collagen
Molecular weight formula_weight	2783.0 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H,I,J

GPPGPPGPPGPPGPRGRTGPPGPPGPPGPP

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2f6aA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1280 —

Domain ID domain_id	2f6aA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	740 —

Domain ID domain_id	2f6aB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1280 —

Domain ID domain_id	2f6aB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	740 —

Domain ID domain_id	2f6aC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1280 —

Domain ID domain_id	2f6aC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	740 —

Domain ID domain_id	2f6aD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1280 —

Domain ID domain_id	2f6aD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	740 —

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8. Citations (1)

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Unit-cell length a length_a	90.547 Å
Unit-cell length b length_b	193.820 Å
Unit-cell length c length_c	205.189 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	48

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.290 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2548
R_work r_work	0.2519
R_free r_free	0.3080

fit	/app/data/saxs_computation/f6/2f6a/2f6a.fit
pddf	/app/data/pr_computation/f6/2f6a/2f6a.pr.out
profile	/app/data/saxs_computation/f6/2f6a/2f6a.dat

Collagen Adhesin and Collagen Complex Structure

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

Collagen adhesin

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)