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5ec6

The apo crystal structure of haemoglobin receptor HpuA from Kingella denitrificans

Method: X-RAY DIFFRACTION Dmax: 65.5 Å Quality: GOOD
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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 21–340 Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；100 mM imidazole, 150 mM lithium sulfate, 6% Peg 3000 Resolution 1.60 Å R-free 0.196

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 5EC6 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5EE4 The crystal structure of HpuA from Kingella denitrificans in complex with human haemoglobin Deposited 2015-10-22 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 21–340（320 aa）
Not recorded 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
5EE4 The crystal structure of HpuA from Kingella denitrificans in complex with human haemoglobin Deposited 2015-10-22 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 21–340（320 aa）
Not recorded 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

1 other PDB entries and 2 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

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 5ec6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5ec6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5ec6
Deposition date deposition_date2015-10-20
Structure title titleThe apo crystal structure of haemoglobin receptor HpuA from Kingella denitrificans
Keywords keywordsOuter membrane, lipoprotein, receptor, beta barrel, metal transport; METAL TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.29 Å
Radius of gyration Rg (electron density) rg_electron19.37 Å
Forward intensity I(0) i019364200.00
Molecular weight molecular_weight31903.0 kDa
Excluded volume excluded_volume39320 ų
Envelope volume envelope_volume46860 ų
Hydration-shell volume shell_volume20255 ų
Envelope diameter envelope_diameter68.0 Å
Shell Rg shell_rg25.78 Å
Envelope Rg envelope_rg19.69 Å
Shape Rg shape_rg19.35 Å
Total Rg total_rg20.26 Å
Total atoms total_atoms2240
Residues n_residues302
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 dmax65.5 Å
Rg (real space) rg_real20.19 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real1.9360e+07
I(0) uncertainty (real space) i0_real_error2.3310e+05
Rg (reciprocal space) rg_reciprocal20.21 Å
I(0) (reciprocal space) i0_reciprocal19360000.0000
Solution quality estimate total_estimate0.8930
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.3 Å
Skewness Skewness skewness0.191
Kurtosis Kurtosis kurtosis-0.392
Angular range angular_range— – 0.3900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3204000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.976
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)