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- PDB-5ee2: The crystal structure of the C-terminal beta-barrel of HpuA from ... -

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Basic information

Entry
Database: PDB / ID: 5ee2
TitleThe crystal structure of the C-terminal beta-barrel of HpuA from Neisseria gonorrhoeae
ComponentsHemoglobin-haptoglobin-utilization protein
KeywordsMETAL TRANSPORT / Outer membrane / lipoprotein / receptor / beta barrel
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
: / 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
Similarity search - Domain/homology
Hemoglobin-haptoglobin-utilization protein
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsWong, C.T. / Hare, S.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)G1100332 United Kingdom
CitationJournal: Nat Commun / Year: 2015
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
DepositionOct 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemoglobin-haptoglobin-utilization protein


Theoretical massNumber of molelcules
Total (without water)16,7701
Polymers16,7701
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.920, 61.920, 92.241
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Hemoglobin-haptoglobin-utilization protein


Mass: 16770.385 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (bacteria)
Gene: NGO_11390 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H4IWK3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 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: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.95-2.063.90.542.3536213920.3140.542.399.9
2.06-2.183.90.3282.3518213260.1890.3283.799.7
2.18-2.3340.2463494512360.1390.246599.9
2.33-2.5240.184.2469511610.1020.186.399.7
2.52-2.7640.1315.6430110770.0750.1318.599.9
2.76-3.0840.0838.238729720.0470.08311.999.9
3.08-3.564.10.05711.134828470.0320.05716.299.9
3.56-4.364.10.05510.129087140.030.05519.799.8
4.36-6.173.90.079721715580.0460.07920.299.6
6.17-30.9640.0351712193030.020.03520.698.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.562
Highest resolutionLowest resolution
Rotation30.96 Å2.17 Å

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
MOLREPphasing
REFMAC5.8.0069refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EC6 residues 168-322

5ec6


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
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 506 5.3 %RANDOM
Rwork0.1781 ---
obs0.1808 9078 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.72 Å2 / Biso mean: 39.259 Å2 / Biso min: 24.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20.45 Å20 Å2
2--0.91 Å20 Å2
3----2.95 Å2
Refinement stepCycle: final / Resolution: 1.95→46.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 0 58 974
Biso mean---45.13 -
Num. residues----122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02929
X-RAY DIFFRACTIONr_bond_other_d0.0010.02867
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9431250
X-RAY DIFFRACTIONr_angle_other_deg0.72231998
X-RAY DIFFRACTIONr_chiral_restr0.080.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02213
X-RAY DIFFRACTIONr_mcbond_it2.5413.561485
X-RAY DIFFRACTIONr_mcbond_other2.5273.556484
X-RAY DIFFRACTIONr_mcangle_it3.5545.307601
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 49 -
Rwork0.278 639 -
all-688 -
obs--99.71 %

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