5ee4

The crystal structure of HpuA from Kingella denitrificans in complex with human haemoglobin

Method: X-RAY DIFFRACTION Dmax: 133.6 Å Quality: GOOD

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

HpuA

Kingella denitrificans ATCC 33394

UniProt F0EX68

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 21–340 Not recorded Hemoglobin subunit alpha × 1 (P69905) Hemoglobin subunit beta × 1 (P68871) GOL GLYCEROL × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;277 K;100 mM Hepes, 18 % Peg 4,000, 10 % Isopropanol Resolution 2.30 Å R-free 0.244
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 21–340 Not recorded Hemoglobin subunit alpha × 1 (P69905) Hemoglobin subunit beta × 1 (P68871) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;277 K;100 mM Hepes, 18 % Peg 4,000, 10 % Isopropanol Resolution 2.30 Å R-free 0.244

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 F0EX68_9NEIS
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–322; UniProt 21–340 Author chain B; PDBConstruct 3–322; UniProt 21–340

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 2–142 Not recorded HpuA × 1 (F0EX68) Hemoglobin subunit beta × 1 (P68871) GOL GLYCEROL × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;277 K;100 mM Hepes, 18 % Peg 4,000, 10 % Isopropanol Resolution 2.30 Å R-free 0.244
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 2–142 Not recorded HpuA × 1 (F0EX68) Hemoglobin subunit beta × 1 (P68871) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;277 K;100 mM Hepes, 18 % Peg 4,000, 10 % Isopropanol Resolution 2.30 Å R-free 0.244

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 411 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HBA_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–141; UniProt 2–142 Author chain E; 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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 2–147 Not recorded HpuA × 1 (F0EX68) Hemoglobin subunit alpha × 1 (P69905) GOL GLYCEROL × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;277 K;100 mM Hepes, 18 % Peg 4,000, 10 % Isopropanol Resolution 2.30 Å R-free 0.244
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 2–147 Not recorded HpuA × 1 (F0EX68) Hemoglobin subunit alpha × 1 (P69905) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 OXY OXYGEN MOLECULE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.8;277 K;100 mM Hepes, 18 % Peg 4,000, 10 % Isopropanol Resolution 2.30 Å R-free 0.244

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 398 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HBB_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 1–146; UniProt 2–147 Author chain F; PDBConstruct 1–146; UniProt 2–147

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 5ee4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5ee4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5ee4
Deposition date deposition_date2015-10-22
Structure title titleThe crystal structure of HpuA from Kingella denitrificans in complex with human haemoglobin
Keywords keywordsOuter membrane, receptor, beta barrel, metal transport; METAL TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier39.45
Radius of gyration Rg (electron density) rg_electron39.35
Forward intensity I(0) i0245410000.00
Molecular weight molecular_weight126810.0 kDa
Excluded volume excluded_volume158350 ų
Envelope volume envelope_volume204050 ų
Hydration-shell volume shell_volume47223 ų
Envelope diameter envelope_diameter140.8
Shell Rg shell_rg40.92
Envelope Rg envelope_rg39.12
Shape Rg shape_rg39.32
Total Rg total_rg39.55
Total atoms total_atoms8934
Residues n_residues1164
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 dmax133.6
Rg (real space) rg_real40.10
Rg uncertainty (real space) rg_real_error1.18
I(0) (real space) i0_real2.4540e+08
I(0) uncertainty (real space) i0_real_error3.9140e+06
Rg (reciprocal space) rg_reciprocal39.70
I(0) (reciprocal space) i0_reciprocal245300000.0000
Solution quality estimate total_estimate0.7686
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary36.7
Skewness Skewness skewness0.654
Kurtosis Kurtosis kurtosis-0.205
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha58270000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.661; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.756; Smooth: 0.248

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5ee4c_
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_idd5ee4d_
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_idd5ee4e_
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_idd5ee4f_
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

CATH v4.4 (4 domains)

Domain ID domain_id5ee4C00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5ee4D00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5ee4E00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id5ee4F00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins

8. Citations (1)

9. Files and Curves (10)