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- PDB-9k1j: Crystal Structure of 6D1-Ab-ohrB complex -

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Basic information

Entry
Database: PDB / ID: 9k1j
TitleCrystal Structure of 6D1-Ab-ohrB complex
ComponentsOrganic hydroperoxide resistance protein
KeywordsOXIDOREDUCTASE / Organic hydroperoxide resistance enzyme
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: 2.09 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 16, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7397
Polymers60,2324
Non-polymers5083
Water5,819323
1
B: Organic hydroperoxide resistance protein
A: Organic hydroperoxide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4544
Polymers30,1162
Non-polymers3382
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Organic hydroperoxide resistance protein
D: Organic hydroperoxide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2853
Polymers30,1162
Non-polymers1691
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15890 Å2
ΔGint-85 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.884, 54.235, 87.853
Angle α, β, γ (deg.)90.00, 107.82, 90.00
Int Tables number4
Space group name H-MP1211

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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: Chemical ChemComp-A1EEB / 6-fluoranyl-1,2-benzothiazol-3-one


Mass: 169.176 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H4FNOS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium formate, 16 % 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 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 38278 / % possible obs: 98.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.059 / Net I/σ(I): 13.3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1907 / Rpim(I) all: 0.399 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.18.1_3865: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→41.82 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 1850 5.14 %
Rwork0.1954 --
obs0.1977 36010 92.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→41.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4216 0 33 323 4572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094319
X-RAY DIFFRACTIONf_angle_d1.1735857
X-RAY DIFFRACTIONf_dihedral_angle_d6.905631
X-RAY DIFFRACTIONf_chiral_restr0.071694
X-RAY DIFFRACTIONf_plane_restr0.008761
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.150.29431120.22531929X-RAY DIFFRACTION68
2.15-2.210.2592930.23662209X-RAY DIFFRACTION78
2.21-2.280.38631380.28222238X-RAY DIFFRACTION80
2.28-2.360.29581320.23062626X-RAY DIFFRACTION93
2.36-2.460.25981410.21352772X-RAY DIFFRACTION97
2.46-2.570.27571560.21542698X-RAY DIFFRACTION97
2.57-2.710.27221660.20622806X-RAY DIFFRACTION100
2.71-2.880.24571490.20532819X-RAY DIFFRACTION99
2.88-3.10.26271390.20982813X-RAY DIFFRACTION99
3.1-3.410.23291530.18992756X-RAY DIFFRACTION97
3.41-3.90.24451500.19072849X-RAY DIFFRACTION99
3.9-4.920.17961560.16172788X-RAY DIFFRACTION97
4.92-41.820.18941650.1612857X-RAY DIFFRACTION97

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