SAXSdb — 5cf3

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

Bone sialoprotein-binding protein

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 272–598	Fragment：UNP residues 272-598	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291.15 K；crystals were grown in 0.2 M calcium acetate hydrate, 0.1 M sodium cacodylate trihydrate pH6.5, 18% PEG8000 Protein concentration was 30mg/ml	Resolution 2.03 Å R-free 0.254

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 5CF3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5CFA Crystal structures of Bbp from Staphylococcus aureus with peptide ligand Deposited 2015-07-08	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 272–598（327 aa） Fragment：UNP residues 272-598	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；peptide was added into the concentrated protein samples at 10:1 ratio and the protein-peptide complex crystals are grown in 0.2 M lithium sulfate, 0.1M Tris-HCl pH8.2, 30% PEG4000 protein concentration was 30mg/ml	Resolution 1.45 Å R-free 0.212
5CFA Crystal structures of Bbp from Staphylococcus aureus with peptide ligand Deposited 2015-07-08	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 272–598（327 aa） Fragment：UNP residues 272-598	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；peptide was added into the concentrated protein samples at 10:1 ratio and the protein-peptide complex crystals are grown in 0.2 M lithium sulfate, 0.1M Tris-HCl pH8.2, 30% PEG4000 protein concentration was 30mg/ml	Resolution 1.45 Å R-free 0.212

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

View Construct and Data Evidence

UniProt name	BBP_STAAU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–331； UniProt 272–598

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	5cf3
Deposition date deposition_date	2015-07-08
Structure title title	Crystal structures of Bbp from Staphylococcus aureus
Keywords keywords	Bbp, Fibrinogen, Sdr, MSCRAMM, PROTEIN BINDING; 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	24.09 Å
Radius of gyration Rg (electron density) rg_electron	23.33 Å
Forward intensity I(0) i0	21733600.00
Molecular weight molecular_weight	35022.0 kDa
Excluded volume excluded_volume	43588 Å³
Envelope volume envelope_volume	53149 Å³
Hydration-shell volume shell_volume	20337 Å³
Envelope diameter envelope_diameter	87.1 Å
Shell Rg shell_rg	28.65 Å
Envelope Rg envelope_rg	23.47 Å
Shape Rg shape_rg	23.30 Å
Total Rg total_rg	24.09 Å
Total atoms total_atoms	2465
Residues n_residues	316
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	85.6 Å
Rg (real space) rg_real	24.29 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	2.1730e+07
I(0) uncertainty (real space) i0_real_error	3.5210e+05
Rg (reciprocal space) rg_reciprocal	24.24 Å
I(0) (reciprocal space) i0_reciprocal	21730000.0000
Solution quality estimate total_estimate	0.8266
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.7 Å
Skewness Skewness skewness	0.539
Kurtosis Kurtosis kurtosis	-0.217
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5468000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.698; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.700; Smooth: 0.948

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Bone sialoprotein-binding protein
Molecular weight formula_weight	36500.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2637

GPLGSNNVNDLITVTKQMITEGIKDDGVIQAHDGEHIIYTSDFKIDNAVKAGDTMTVKYDKHTIPSDITDDFTPVDITDPSGEVIAKGTFDLNTKTITYKFTDYVDRYENVNAKLELNSYIDKKEVPNETNLNLTFATADKETSKNVKVEYQKPIVKDESNIQSIFSHLDTTKHEVEQTIYVNPLKLNAKNTNVTIKSGGVADNGDYYTGDGSTIIDSNTEIKVYKVASGQQLPQSNKIYDYSQYEDVTNSVTINKNYGTNMANINFGDIDSAYIVKVVSKYTPGAEDDLAVQQGVRMTTTNKYNYSSYAGYTNTILSTTDSGGGDGTVKP

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 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	172

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5cf3a1
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.3 — Bacterial adhesins
Family Family family	b.2.3.0 — automated matches

Domain ID domain_id	d5cf3a2
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.3 — Bacterial adhesins
Family Family family	b.2.3.0 — automated matches

Domain ID domain_id	d5cf3a3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	5cf3A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1280 —

Domain ID domain_id	5cf3A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1290 —

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8. Citations (1)

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Unit-cell length a length_a	96.241 Å
Unit-cell length b length_b	98.924 Å
Unit-cell length c length_c	102.257 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.031 Å
Low-resolution limit resolution_low	28.593 Å
R factor r_factor	0.2185
R_work r_work	0.2166
R_free r_free	0.2535

fit	/app/data/saxs_computation/cf/5cf3/5cf3.fit
pddf	/app/data/pr_computation/cf/5cf3/5cf3.pr.out
profile	/app/data/saxs_computation/cf/5cf3/5cf3.dat

Crystal structures of Bbp from Staphylococcus aureus

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

Bone sialoprotein-binding protein

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