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- PDB-9jxc: Crystal Structure of AbOhr-R15C -

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Basic information

Entry
Database: PDB / ID: 9jxc
TitleCrystal Structure of AbOhr-R15C
ComponentsOrganic hydroperoxide resistance protein
KeywordsOXIDOREDUCTASE / organic hydroperoxide resistance / R15C mutation
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)60,0154
Polymers60,0154
Non-polymers00
Water3,423190
1
B: Organic hydroperoxide resistance protein
A: Organic hydroperoxide resistance protein


Theoretical massNumber of molelcules
Total (without water)30,0082
Polymers30,0082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-43 kcal/mol
Surface area12980 Å2
MethodPISA
2
C: Organic hydroperoxide resistance protein
D: Organic hydroperoxide resistance protein


Theoretical massNumber of molelcules
Total (without water)30,0082
Polymers30,0082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-44 kcal/mol
Surface area12980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.129, 51.348, 82.047
Angle α, β, γ (deg.)90.00, 103.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Organic hydroperoxide resistance protein


Mass: 15003.864 Da / Num. of mol.: 4 / Mutation: R15C
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.: 190 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M AMMONIUM SULFATE, 18 % w/v Polyethylene glycol 3350, 0.1 M MES pH 6.0

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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: 2.1→39.88 Å / Num. obs: 33504 / % possible obs: 96 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Net I/σ(I): 14.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 6.2 / Num. unique obs: 3328 / Rpim(I) all: 0.096 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→43.21 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.972 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25746 1653 4.9 %RANDOM
Rwork0.20348 ---
obs0.20615 31880 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.266 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å2-0 Å2-0.82 Å2
2--2.7 Å2-0 Å2
3----2.49 Å2
Refinement stepCycle: 1 / Resolution: 2.1→43.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4144 0 0 190 4334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134192
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173922
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.6345680
X-RAY DIFFRACTIONr_angle_other_deg1.3521.5759108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2235556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5724.239184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.16115702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4111516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024740
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02780
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2983.4952242
X-RAY DIFFRACTIONr_mcbond_other3.2993.4942241
X-RAY DIFFRACTIONr_mcangle_it4.965.2182792
X-RAY DIFFRACTIONr_mcangle_other4.9595.2192793
X-RAY DIFFRACTIONr_scbond_it3.8994.0791950
X-RAY DIFFRACTIONr_scbond_other3.8984.081951
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other65.852889
X-RAY DIFFRACTIONr_long_range_B_refined8.6142.594433
X-RAY DIFFRACTIONr_long_range_B_other8.61442.5474413
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å
RfactorNum. reflection% reflection
Rfree0.289 127 -
Rwork0.229 2330 -
obs--96.66 %

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