SAXSdb — 2j5y

▼

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

PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN

PEPTOSTREPTOCOCCUS MAGNUS

UniProt Q51911

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 213–265	Fragment：ALBUMIN-BINDING DOMAIN, RESIDUES 213-265	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；22-26% (W/V) PEG 3350, 50 MM POTASSIUM PHOSPHATE PH 7.5, 100 MM AMMONIUM ACETATE	Resolution 1.40 Å R-free 0.199
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 213–265	Fragment：ALBUMIN-BINDING DOMAIN, RESIDUES 213-265	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；22-26% (W/V) PEG 3350, 50 MM POTASSIUM PHOSPHATE PH 7.5, 100 MM AMMONIUM ACETATE	Resolution 1.40 Å R-free 0.199

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 2J5Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GAB STRUCTURE OF AN ALBUMIN-BINDING DOMAIN, NMR, 20 STRUCTURES Deposited 1996-12-30	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 213–265（53 aa） Fragment：ALBUMIN-BINDING DOMAIN, RESIDUES 213 - 265	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；300 K	Resolution not provided
1PRB STRUCTURE OF AN ALBUMIN-BINDING DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-01-15	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 213–265（53 aa） Fragment：ALBUMIN-BINDING DOMAIN, RESIDUES 213 - 265	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；300 K	Resolution not provided
1TF0 Crystal structure of the GA module complexed with human serum albumin Deposited 2004-05-26	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 213–265（53 aa）	Not recorded	DKA DECANOIC ACID × 3 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；Ammonium sulfate, citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.295
2VDB Structure of human serum albumin with S-naproxen and the GA module Deposited 2007-10-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 213–265（53 aa） Fragment：RESIDUES 213-265	Not recorded	DKA DECANOIC ACID × 6 NPS (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions 26-32% PEG 3350, 50 MM POTASSIUM PHOSPHATE, 0.1 M AMMONIUM PHOSPHATE/POTASSIUM PHOSPHATE	Resolution 2.52 Å R-free 0.280
9BB1 Backbone Modification in the GA Module of Protein PAB: Wild-type Sequence Deposited 2024-04-05	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 219–265（47 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.3；300 K；Ionic strength (raw mmCIF value) 1；Pressure 1 NMR sample composition 1 mM GA Module of Protein PAB, 0.2 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9BB2 Backbone Modification in the GA Module of Protein PAB: beta3-residues at positions 20 and 24 Deposited 2024-04-05	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 219–265（47 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；283 K；Ionic strength (raw mmCIF value) 1；Pressure 1 NMR sample composition 1 mM GA Module of Protein PAB: beta3 residues at positions 20 and 24, 0.2 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9BB3 Backbone Modification in the GA Module of Protein PAB: beta3-residues at positions 22 and 26 Deposited 2024-04-05	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 219–265（47 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 1；Pressure 1 NMR sample composition 1 mM GA Module of Protein PAB: beta3 residues at positions 22 and 26, 0.2 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9BB4 Backbone Modification in the GA Module of Protein PAB: beta3-residues at positions 23 and 26 Deposited 2024-04-05	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 219–265（47 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.9；283 K；Ionic strength (raw mmCIF value) 1；Pressure 1 NMR sample composition 1 mM GA Module of Protein PAB: beta3 residues at positions 23 and 26, 0.2 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9BB5 Backbone Modification in the GA Module of Protein PAB: ACPC residues at positions 22 and 26 Deposited 2024-04-05	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 219–265（47 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.9；283 K；Ionic strength (raw mmCIF value) 1；Pressure 1 NMR sample composition 1 mM GA Module of Protein PAB: ACPC residues at positions 22 and 26, 0.2 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9BB6 Backbone Modification in the GA Module of Protein PAB: ACPC residues at positions 5 and 13, beta3 residue at position 9 Deposited 2024-04-05	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 219–265（47 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.8；283 K；Ionic strength (raw mmCIF value) 1；Pressure 1 NMR sample composition 1 mM GA Module of Protein PAB: ACPC residues at positions 5 and 13, beta3 residue at position 9, 0.2 mM dss, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9BB7 Backbone Modification in the GA Module of Protein PAB: ACPC residues at positions 5 and 39, beta3 residue at position 26 Deposited 2024-04-05	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 219–265（47 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.6；300 K；Ionic strength (raw mmCIF value) 1；Pressure 1 NMR sample composition 0.88 mM GA Module of Protein PAB: ACPC residues at positions 5 and 39, beta3 residue at position 26, 0.19 mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PAB_PEPMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–61； UniProt 213–265 Author chain B； PDBConstruct 9–61； UniProt 213–265

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2j5y
Deposition date deposition_date	2006-09-20
Structure title title	Crystal structure of the GA module from F.magna
Keywords keywords	PROTEIN BINDING, CELL WALL, PEPTIDOGLYCAN-ANCHOR, PROTEIN BINDING BACTERIAL ALBUMIN-BINDING THREE-HELIX BUNDLE; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	17.18 Å
Radius of gyration Rg (electron density) rg_electron	16.25 Å
Forward intensity I(0) i0	3487320.00
Molecular weight molecular_weight	13620.0 kDa
Excluded volume excluded_volume	17279 Å³
Envelope volume envelope_volume	20940 Å³
Hydration-shell volume shell_volume	11620 Å³
Envelope diameter envelope_diameter	52.7 Å
Shell Rg shell_rg	20.88 Å
Envelope Rg envelope_rg	16.38 Å
Shape Rg shape_rg	16.26 Å
Total Rg total_rg	17.19 Å
Total atoms total_atoms	960
Residues n_residues	122
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	54.1 Å
Rg (real space) rg_real	17.15 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	3.4870e+06
I(0) uncertainty (real space) i0_real_error	4.3160e+04
Rg (reciprocal space) rg_reciprocal	17.16 Å
I(0) (reciprocal space) i0_reciprocal	3487000.0000
Solution quality estimate total_estimate	0.9036
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.4 Å
Skewness Skewness skewness	0.201
Kurtosis Kurtosis kurtosis	-0.580
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	649500.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.998

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2j5ya2
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.1 — Bacterial immunoglobulin/albumin-binding domains
Family Family family	a.8.1.2 — GA module, an albumin-binding domain

Domain ID domain_id	d2j5ya3
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

Domain ID domain_id	d2j5yb2
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.1 — Bacterial immunoglobulin/albumin-binding domains
Family Family family	a.8.1.2 — GA module, an albumin-binding domain

Domain ID domain_id	d2j5yb3
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	2j5yA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	40 — Albumin-binding domain

Domain ID domain_id	2j5yB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	40 — Albumin-binding domain

▶

8. Citations (2)

▶

Unit-cell length a length_a	25.784 Å
Unit-cell length b length_b	58.068 Å
Unit-cell length c length_c	40.570 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	40.560 Å
R factor r_factor	0.1510
R_work r_work	0.1480
R_free r_free	0.1990

Description description	PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN
Molecular weight formula_weight	6819.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1221

Crystal structure of the GA module from F.magna

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

PEPTOSTREPTOCOCCAL ALBUMIN-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

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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	PEPTOSTREPTOCOCCUS MAGNUS
NCBI Class编号 ncbi_taxonomy_id	1260
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	183

fit	/app/data/saxs_computation/j5/2j5y/2j5y.fit
pddf	/app/data/pr_computation/j5/2j5y/2j5y.pr.out
profile	/app/data/saxs_computation/j5/2j5y/2j5y.dat