4ij2

Human methemoglobin in complex with the second and third NEAT domains of IsdH from Staphylococcus aureus

Method: X-RAY DIFFRACTION Dmax: 127.8 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 surface determinant protein H × 4 (Q2FG07) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;294 K;0.2M diammonium citrate, 13%(w/v) PEG3350, 0.7% 1-butanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 4.24 Å R-free 0.310

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 surface determinant protein H × 4 (Q2FG07) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;294 K;0.2M diammonium citrate, 13%(w/v) PEG3350, 0.7% 1-butanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 4.24 Å R-free 0.310

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 surface determinant protein H

Staphylococcus aureus

UniProt Q2FG07

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 326–660 Chain F; UniProt 326–660 Chain G; UniProt 326–660 Chain H; UniProt 326–660 Fragment:NEAT2, NEAT3, UNP residues 326-660 Mutation:Y642A 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 4.6;294 K;0.2M diammonium citrate, 13%(w/v) PEG3350, 0.7% 1-butanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 4.24 Å R-free 0.310

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.

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

View Construct and Data Evidence
UniProt name ISDH_STAA3
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 2–336; UniProt 326–660 Author chain F; PDBConstruct 2–336; UniProt 326–660 Author chain G; PDBConstruct 2–336; UniProt 326–660 Author chain H; PDBConstruct 2–336; UniProt 326–660

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 4ij2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ij2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4ij2
Deposition date deposition_date2012-12-21
Structure title titleHuman methemoglobin in complex with the second and third NEAT domains of IsdH from Staphylococcus aureus
Keywords keywordsNEAT, Heme/Hemoglobin binding, Hemoglobin, Cell wall associated, 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_guinier40.43
Radius of gyration Rg (electron density) rg_electron39.77
Forward intensity I(0) i0514071000.00
Molecular weight molecular_weight191750.0 kDa
Excluded volume excluded_volume242470 ų
Envelope volume envelope_volume348930 ų
Hydration-shell volume shell_volume71083 ų
Envelope diameter envelope_diameter135.1
Shell Rg shell_rg47.15
Envelope Rg envelope_rg39.37
Shape Rg shape_rg39.77
Total Rg total_rg40.21
Total atoms total_atoms13545
Residues n_residues1674
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 dmax127.8
Rg (real space) rg_real40.23
Rg uncertainty (real space) rg_real_error0.90
I(0) (real space) i0_real5.1410e+08
I(0) uncertainty (real space) i0_real_error7.6960e+06
Rg (reciprocal space) rg_reciprocal40.43
I(0) (reciprocal space) i0_reciprocal514200000.0000
Solution quality estimate total_estimate0.8890
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary52.4
Skewness Skewness skewness0.137
Kurtosis Kurtosis kurtosis-0.428
Angular range angular_range— – 0.1950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha66460000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.881; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.932

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)