5vmm

Staphylococcus aureus IsdB bound to human hemoglobin

Method: X-RAY DIFFRACTION Dmax: 124.0 Å Quality: GOOD

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

Hemoglobin subunit alpha

OrganismNot specified

UniProt P69905

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 2–142 Chain C; UniProt 2–142 Not recorded Hemoglobin subunit beta × 2 (P68871) Iron-regulated cell wall-anchored protein × 2 (A0A1K8PKR3) Iron-regulated cell wall-anchored protein × 2 (A0A1K8PKR3) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;298 K;0.1 M malonic acid pH 5.5, 2.2 M ammonium sulfate Resolution 3.60 Å R-free 0.302

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.

348 other PDB entries and 412 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HBA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–141; UniProt 2–142 Author chain C; PDBConstruct 1–141; UniProt 2–142

Hemoglobin subunit beta

OrganismNot specified

UniProt P68871

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain B; UniProt 2–147 Chain D; UniProt 2–147 Not recorded Hemoglobin subunit alpha × 2 (P69905) Iron-regulated cell wall-anchored protein × 2 (A0A1K8PKR3) Iron-regulated cell wall-anchored protein × 2 (A0A1K8PKR3) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;298 K;0.1 M malonic acid pH 5.5, 2.2 M ammonium sulfate Resolution 3.60 Å R-free 0.302

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.

343 other PDB entries and 399 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HBB_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–146; UniProt 2–147 Author chain D; PDBConstruct 1–146; UniProt 2–147

Iron-regulated cell wall-anchored protein

Staphylococcus aureus

UniProt A0A1K8PKR3

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 × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain E; UniProt 125–458 Chain F; UniProt 125–458 Chain H; UniProt 125–264 Chain J; UniProt 125–264 Fragment:UNP residues 125-458 Fragment:UNP residues 125-264 Hemoglobin subunit alpha × 2 (P69905) Hemoglobin subunit beta × 2 (P68871) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;298 K;0.1 M malonic acid pH 5.5, 2.2 M ammonium sulfate Resolution 3.60 Å R-free 0.302

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A1K8PKR3_STAAU
Isoform
PDB entities 3, 4
Chains and sequence ranges Author chain E; PDBConstruct 3–336; UniProt 125–458 Author chain F; PDBConstruct 3–336; UniProt 125–458 Author chain H; PDBConstruct 3–142; UniProt 125–264 Author chain J; PDBConstruct 3–142; UniProt 125–264

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 5vmm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5vmm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5vmm
Deposition date deposition_date2017-04-27
Structure title titleStaphylococcus aureus IsdB bound to human hemoglobin
Keywords keywordsheme transfer, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier39.37
Radius of gyration Rg (electron density) rg_electron38.62
Forward intensity I(0) i0403040000.00
Molecular weight molecular_weight167440.0 kDa
Excluded volume excluded_volume211160 ų
Envelope volume envelope_volume289750 ų
Hydration-shell volume shell_volume62260 ų
Envelope diameter envelope_diameter130.6
Shell Rg shell_rg44.73
Envelope Rg envelope_rg38.46
Shape Rg shape_rg38.59
Total Rg total_rg39.10
Total atoms total_atoms11827
Residues n_residues1470
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax124.0
Rg (real space) rg_real39.16
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real4.0300e+08
I(0) uncertainty (real space) i0_real_error6.2040e+06
Rg (reciprocal space) rg_reciprocal39.29
I(0) (reciprocal space) i0_reciprocal403100000.0000
Solution quality estimate total_estimate0.8905
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary52.7
Skewness Skewness skewness0.176
Kurtosis Kurtosis kurtosis-0.393
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha59610000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.843

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id5vmmA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5vmmB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5vmmC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5vmmD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5vmmE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1850
Domain ID domain_id5vmmE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1850
Domain ID domain_id5vmmH00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1850
Domain ID domain_id5vmmJ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1850

8. Citations (1)

9. Files and Curves (10)