SAXSdb — 1d2p

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 533–905	Fragment：B REPEAT REGIONS	No other associated polymer	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

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 1D2P	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 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 mutation/modification 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
2F68 Crystal structure of collagen adhesin (CNA) from S. aureus Deposited 2005-11-28	Different construct 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
2F6A Collagen Adhesin and Collagen Complex Structure Deposited 2005-11-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 30–330（301 aa） Fragment：extracellular domain Chain C 30–330（301 aa） Fragment：extracellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.35；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
2F6A Collagen Adhesin and Collagen Complex Structure Deposited 2005-11-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 30–330（301 aa） Fragment：extracellular domain Chain D 30–330（301 aa） Fragment：extracellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.35；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
2F6A Collagen Adhesin and Collagen Complex Structure Deposited 2005-11-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain A 30–330（301 aa） Fragment：extracellular domain Chain B 30–330（301 aa） Fragment：extracellular domain Chain C 30–330（301 aa） Fragment：extracellular domain Chain D 30–330（301 aa） Fragment：extracellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.35；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

4 other PDB entries and 6 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 1–373； UniProt 533–905

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	1d2p
Deposition date deposition_date	1999-09-25
Structure title title	CRYSTAL STRUCTURE OF TWO B REPEAT UNITS (B1B2) OF THE COLLAGEN BINDING PROTEIN (CNA) OF STAPHYLOCOCCUS AUREUS
Keywords keywords	COLLAGEN, IGG, IGSF, MSCRAMM, CNA, STAPHYLOCOCCUS AUREUS, STRUCTURAL PROTEIN; 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	30.47 Å
Radius of gyration Rg (electron density) rg_electron	30.47 Å
Forward intensity I(0) i0	31715600.00
Molecular weight molecular_weight	42341.0 kDa
Excluded volume excluded_volume	52298 Å³
Envelope volume envelope_volume	69723 Å³
Hydration-shell volume shell_volume	21022 Å³
Envelope diameter envelope_diameter	107.0 Å
Shell Rg shell_rg	34.08 Å
Envelope Rg envelope_rg	30.23 Å
Shape Rg shape_rg	30.45 Å
Total Rg total_rg	30.89 Å
Total atoms total_atoms	2986
Residues n_residues	373
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	102.1 Å
Rg (real space) rg_real	30.86 Å
Rg uncertainty (real space) rg_real_error	1.00 Å
I(0) (real space) i0_real	3.1720e+07
I(0) uncertainty (real space) i0_real_error	5.3350e+05
Rg (reciprocal space) rg_reciprocal	30.70 Å
I(0) (reciprocal space) i0_reciprocal	31710000.0000
Solution quality estimate total_estimate	0.7721
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.6 Å
Skewness Skewness skewness	0.495
Kurtosis Kurtosis kurtosis	-0.616
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3874000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.658; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.398; Smooth: 0.660

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1d2pa1
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.5 — Cna protein B-type domain
Family Family family	b.3.5.1 — Cna protein B-type domain

Domain ID domain_id	d1d2pa2
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.5 — Cna protein B-type domain
Family Family family	b.3.5.1 — Cna protein B-type domain

Domain ID domain_id	d1d2pa3
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.5 — Cna protein B-type domain
Family Family family	b.3.5.1 — Cna protein B-type domain

Domain ID domain_id	d1d2pa4
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.5 — Cna protein B-type domain
Family Family family	b.3.5.1 — Cna protein B-type domain

CATH v4.4 (4 domains)

Domain ID domain_id	1d2pA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1140 — Collagen-binding surface protein Cna, B-type domain

Domain ID domain_id	1d2pA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1140 — Collagen-binding surface protein Cna, B-type domain

Domain ID domain_id	1d2pA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1140 — Collagen-binding surface protein Cna, B-type domain

Domain ID domain_id	1d2pA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1140 — Collagen-binding surface protein Cna, B-type domain

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8. Citations (1)

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Unit-cell length a length_a	42.392 Å
Unit-cell length b length_b	79.418 Å
Unit-cell length c length_c	130.399 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	4

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	19.950 Å
R factor r_factor	0.1850
R_work r_work	0.1850
R_free r_free	0.2450

Description description	COLLAGEN ADHESIN
Molecular weight formula_weight	42413.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3061

CRYSTAL STRUCTURE OF TWO B REPEAT UNITS (B1B2) OF THE COLLAGEN BINDING PROTEIN (CNA) OF STAPHYLOCOCCUS AUREUS

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 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	75

fit	/app/data/saxs_computation/d2/1d2p/1d2p.fit
pddf	/app/data/pr_computation/d2/1d2p/1d2p.pr.out
profile	/app/data/saxs_computation/d2/1d2p/1d2p.dat