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- PDB-1zb9: Crystal structure of Xylella fastidiosa organic peroxide resistan... -

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Basic information

Entry
Database: PDB / ID: 1zb9
TitleCrystal structure of Xylella fastidiosa organic peroxide resistance protein
Componentsorganic hydroperoxide resistance protein
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


response to oxidative stress
Similarity search - Function
Organic hydroperoxide resistance protein famiy / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / GMP Synthetase; Chain A, domain 3 / Single Sheet / K homology domain-like, alpha/beta ...Organic hydroperoxide resistance protein famiy / OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / GMP Synthetase; Chain A, domain 3 / Single Sheet / K homology domain-like, alpha/beta / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Organic hydroperoxide resistance protein
Similarity search - Component
Biological speciesXylella fastidiosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOliveira, M.A. / Guimaraes, B.G. / Cussiol, J.R. / Medrano, F.J. / Vidigal, S.A. / Gozzo, F.C. / Netto, L.E.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Insights into Enzyme-Substrate Interaction and Characterization of Enzymatic Intermediates of Organic Hydroperoxide Resistance Protein from Xylella fastidiosa.
Authors: Oliveira, M.A. / Guimaraes, B.G. / Cussiol, J.R. / Medrano, F.J. / Gozzo, F.C. / Netto, L.E.
History
DepositionApr 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: organic hydroperoxide resistance protein
B: organic hydroperoxide resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6314
Polymers29,9222
Non-polymers7092
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-41 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.655, 87.655, 160.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biologial assembly is the asymmetric unit (dimer).

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Components

#1: Protein organic hydroperoxide resistance protein / ohr


Mass: 14961.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xylella fastidiosa (bacteria) / Strain: 9a5c / Gene: ohr / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9PCF4
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.8 Å3/Da / Density % sol: 55.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: Peg 4000, Tris-HCl, 5mM t-BOOH, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.453 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 5, 2003 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.453 Å / Relative weight: 1
ReflectionResolution: 1.8→1.88 Å / Num. obs: 34330 / % possible obs: 99.9 % / Redundancy: 10.8 % / Rsym value: 0.074 / Net I/σ(I): 6.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 4391 / Rsym value: 0.328 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→1.88 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2142 1714 -Random
Rwork0.1963 ---
all-34330 --
obs-32616 94.5 %-
Refinement stepCycle: LAST / Resolution: 1.8→1.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 34 256 2339
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it1.2191.5
X-RAY DIFFRACTIONo_mcangle_it1.9592
X-RAY DIFFRACTIONo_scbond_it1.9392
X-RAY DIFFRACTIONo_scangle_it2.8362.5
LS refinement shellResolution: 1.8→1.88 Å
RfactorNum. reflection% reflection
Rfree0.3385 211 -
Rwork0.2929 --
obs-3989 99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep1.paramprotein_CSX.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5PE4_1.paramPE4_1.top

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