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- PDB-5ee2: The crystal structure of the C-terminal beta-barrel of HpuA from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ee2 | ||||||
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Title | The crystal structure of the C-terminal beta-barrel of HpuA from Neisseria gonorrhoeae | ||||||
![]() | Hemoglobin-haptoglobin-utilization protein | ||||||
![]() | METAL TRANSPORT / Outer membrane / lipoprotein / receptor / beta barrel | ||||||
Function / homology | Haemoglobin-haptoglobin utilisation, porphyrin transporter / Haemoglobin-haptoglobin utilisation, porphyrin transporter / Porin - #90 / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta / Hemoglobin-haptoglobin-utilization protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Wong, C.T. / Hare, S.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analysis of haemoglobin binding by HpuA from the Neisseriaceae family. Authors: Wong, C.T. / Xu, Y. / Gupta, A. / Garnett, J.A. / Matthews, S.J. / Hare, S.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39 KB | Display | ![]() |
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PDB format | ![]() | 25.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419.3 KB | Display | ![]() |
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Full document | ![]() | 420.4 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 9.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ec6SC ![]() 5ee4C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16770.385 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: NGO_11390 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 100 mM Hepes, 1.6 M ammonium sulfate, 0.8 % Peg 400, 200 mM sodium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→46.36 Å / Num. all: 9586 / Num. obs: 9586 / % possible obs: 99.8 % / Redundancy: 4 % / Rpim(I) all: 0.047 / Rrim(I) all: 0.096 / Rsym value: 0.084 / Net I/av σ(I): 5.232 / Net I/σ(I): 9.1 / Num. measured all: 38137 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | R rigid body: 0.562
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5EC6 residues 168-322 Resolution: 1.95→46.36 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2322 / WRfactor Rwork: 0.1829 / FOM work R set: 0.8319 / SU B: 4.115 / SU ML: 0.113 / SU R Cruickshank DPI: 0.1535 / SU Rfree: 0.1499 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 98.72 Å2 / Biso mean: 39.259 Å2 / Biso min: 24.53 Å2
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Refinement step | Cycle: final / Resolution: 1.95→46.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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