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1prb

STRUCTURE OF AN ALBUMIN-BINDING DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE

Method: SOLUTION NMR Dmax: 45.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN PAB

Finegoldia magna ATCC 29328

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 SOLUTION NMR NMR measurement conditions：pH 6；300 K Resolution not provided

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 1PRB 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 Parsed fields agree 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 method 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
2J5Y Crystal structure of the GA module from F.magna Deposited 2006-09-20 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 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
2J5Y Crystal structure of the GA module from F.magna Deposited 2006-09-20 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 213–265（53 aa） Fragment：ALBUMIN-BINDING DOMAIN, RESIDUES 213-265
Not recorded No recorded non-water small molecule 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
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 method 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 conditions 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 conditions 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 conditions 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 conditions 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 conditions 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 conditions 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 conditions 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 12 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 1–53； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 1prb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1prb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1prb
Deposition date deposition_date1997-01-15
Structure title titleSTRUCTURE OF AN ALBUMIN-BINDING DOMAIN, NMR, MINIMIZED AVERAGE STRUCTURE
Keywords keywordsALBUMIN-BINDING PROTEIN, BACTERIAL SURFACE PROTEINS, EVOLUTION, MODULE SHUFFLING; ALBUMIN-BINDING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.47 Å
Radius of gyration Rg (electron density) rg_electron11.26 Å
Forward intensity I(0) i0800957.00
Molecular weight molecular_weight5931.0 kDa
Excluded volume excluded_volume7551 ų
Envelope volume envelope_volume8450 ų
Hydration-shell volume shell_volume7005 ų
Envelope diameter envelope_diameter43.5 Å
Shell Rg shell_rg15.80 Å
Envelope Rg envelope_rg11.82 Å
Shape Rg shape_rg11.22 Å
Total Rg total_rg12.73 Å
Total atoms total_atoms851
Residues n_residues53
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 dmax45.5 Å
Rg (real space) rg_real12.51 Å
Rg uncertainty (real space) rg_real_error0.46 Å
I(0) (real space) i0_real8.0100e+05
I(0) uncertainty (real space) i0_real_error8.4900e+03
Rg (reciprocal space) rg_reciprocal12.51 Å
I(0) (reciprocal space) i0_reciprocal801000.0000
Solution quality estimate total_estimate0.8070
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary14.4 Å
Skewness Skewness skewness0.494
Kurtosis Kurtosis kurtosis0.230
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha156800.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.544; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.915; Smooth: 0.944
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1prba_
Class classa — All alpha proteins
Fold Fold folda.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamilya.8.1 — Bacterial immunoglobulin/albumin-binding domains
Family Family familya.8.1.2 — GA module, an albumin-binding domain

CATH v4.4 (1 domains)

Domain ID domain_id1prbA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily40 — Albumin-binding domain
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8. Citations (2)

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9. Files and Curves (10)