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- PDB-9jx6: Crystal Structure of wild type Ab-ohrB -

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Basic information

Entry
Database: PDB / ID: 9jx6
TitleCrystal Structure of wild type Ab-ohrB
ComponentsOrganic hydroperoxide resistance protein
KeywordsOXIDOREDUCTASE / Organic hydroperoxide resistance protein-like 2 / Apo
Function / homologyOrganic hydroperoxide resistance protein famiy / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology domain-like, alpha/beta / response to oxidative stress / Organic hydroperoxide resistance protein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHuang, W. / Hu, C.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To be published
Title: Crystal Structure of 6D1-Ab-ohrB complex
Authors: Huang, W. / Hu, C.X.
History
DepositionOct 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Organic hydroperoxide resistance protein
A: Organic hydroperoxide resistance protein
C: Organic hydroperoxide resistance protein
D: Organic hydroperoxide resistance protein


Theoretical massNumber of molelcules
Total (without water)60,2324
Polymers60,2324
Non-polymers00
Water4,846269
1
B: Organic hydroperoxide resistance protein
A: Organic hydroperoxide resistance protein


Theoretical massNumber of molelcules
Total (without water)30,1162
Polymers30,1162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-43 kcal/mol
Surface area12510 Å2
MethodPISA
2
C: Organic hydroperoxide resistance protein
D: Organic hydroperoxide resistance protein


Theoretical massNumber of molelcules
Total (without water)30,1162
Polymers30,1162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-43 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.886, 53.561, 87.753
Angle α, β, γ (deg.)90.000, 107.380, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein
Organic hydroperoxide resistance protein


Mass: 15057.915 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ohr / Production host: Escherichia coli (E. coli) / References: UniProt: Q5DQT1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M LiCl, 18 % w/v Polyethylene glycol 3350, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 37202 / % possible obs: 98.5 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.056 / Net I/σ(I): 14.1
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 1.01 / Num. unique obs: 1847 / Rpim(I) all: 0.38

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→22.56 Å / SU ML: 0.254 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.3999
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 1733 4.96 %RANDOM
Rwork0.2103 33220 --
obs0.2126 34953 93.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.97 Å2
Refinement stepCycle: LAST / Resolution: 2.1→22.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4177 0 0 269 4446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034227
X-RAY DIFFRACTIONf_angle_d0.54345727
X-RAY DIFFRACTIONf_chiral_restr0.0443687
X-RAY DIFFRACTIONf_plane_restr0.0036744
X-RAY DIFFRACTIONf_dihedral_angle_d5.1618597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.30561100.25031701X-RAY DIFFRACTION58.7
2.16-2.230.30251470.25072446X-RAY DIFFRACTION82.84
2.23-2.310.31071230.23912804X-RAY DIFFRACTION94.82
2.31-2.40.27791440.2272885X-RAY DIFFRACTION97.74
2.4-2.510.30071480.23812840X-RAY DIFFRACTION96.26
2.51-2.650.28731600.23172939X-RAY DIFFRACTION99.49
2.65-2.810.25221370.21722957X-RAY DIFFRACTION99.26
2.81-3.030.30791460.22072932X-RAY DIFFRACTION99
3.03-3.330.26881640.20772893X-RAY DIFFRACTION97.33
3.33-3.810.21471500.19862961X-RAY DIFFRACTION99.2
3.81-4.790.19961480.18482894X-RAY DIFFRACTION96.39
4.79-22.560.25411560.19182968X-RAY DIFFRACTION97.11

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