4fc3

Crystal Structure of Human Methaemoglobin Complexed with the Second NEAT Domain of IsdH from Staphylococcus aureus

Method: X-RAY DIFFRACTION Dmax: 85.1 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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 2–142 Not recorded Hemoglobin subunit beta × 2 (P68871) Iron-regulated surface determinant protein H × 2 (Q8NW39) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.2M Sodium formate, 0.1M bis-tris propane, 20% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.26 Å R-free 0.256

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

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 2–147 Not recorded Hemoglobin subunit alpha × 2 (P69905) Iron-regulated surface determinant protein H × 2 (Q8NW39) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.2M Sodium formate, 0.1M bis-tris propane, 20% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.26 Å R-free 0.256

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

Iron-regulated surface determinant protein H

Staphylococcus aureus

UniProt Q8NW39

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain E; UniProt 321–464 Fragment:Second NEAT domain Hemoglobin subunit alpha × 2 (P69905) Hemoglobin subunit beta × 2 (P68871) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;293 K;0.2M Sodium formate, 0.1M bis-tris propane, 20% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.26 Å R-free 0.256

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.

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ISDH_STAAW
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 21–164; UniProt 321–464

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 4fc3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4fc3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4fc3
Deposition date deposition_date2012-05-24
Structure title titleCrystal Structure of Human Methaemoglobin Complexed with the Second NEAT Domain of IsdH from Staphylococcus aureus
Keywords keywords;Globin Fold, Ig Fold, Oxygen Transport, Haem acquisition, Oxygen Binding, Haem binding, cell wall, OXYGEN TRANSPORT-PROTEIN BINDING complex ;; OXYGEN TRANSPORT/PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.39
Radius of gyration Rg (electron density) rg_electron24.54
Forward intensity I(0) i035881000.00
Molecular weight molecular_weight47759.0 kDa
Excluded volume excluded_volume60341 ų
Envelope volume envelope_volume72533 ų
Hydration-shell volume shell_volume25327 ų
Envelope diameter envelope_diameter89.3
Shell Rg shell_rg31.17
Envelope Rg envelope_rg24.84
Shape Rg shape_rg24.53
Total Rg total_rg25.37
Total atoms total_atoms3378
Residues n_residues427
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 dmax85.1
Rg (real space) rg_real25.44
Rg uncertainty (real space) rg_real_error0.65
I(0) (real space) i0_real3.5880e+07
I(0) uncertainty (real space) i0_real_error4.9100e+05
Rg (reciprocal space) rg_reciprocal25.43
I(0) (reciprocal space) i0_reciprocal35880000.0000
Solution quality estimate total_estimate0.8757
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.0
Skewness Skewness skewness0.429
Kurtosis Kurtosis kurtosis-0.247
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7899000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.931; Smooth: 0.923

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd4fc3a_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins
Domain ID domain_idd4fc3b_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins
Domain ID domain_idd4fc3e_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.28 — NEAT domain-like
Family Family familyb.1.28.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id4fc3A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id4fc3B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id4fc3E00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1850

8. Citations (1)

9. Files and Curves (10)