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- PDB-3wl5: Crystal structure of pOPH S172C -

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Basic information

Entry
Database: PDB / ID: 3wl5
TitleCrystal structure of pOPH S172C
ComponentsOxidized polyvinyl alcohol hydrolase
KeywordsHYDROLASE / alpha/beta-hydrolase / oxi-polyvinyl alcohol hydrolase
Function / homologybeta-diketone hydrolase / beta-diketone hydrolase activity / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / CITRIC ACID / Oxidized polyvinyl alcohol hydrolase
Function and homology information
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsYang, Y. / Ko, T.P. / Li, J.H. / Liu, L. / Huang, C.H. / Chan, H.C. / Ren, F.F. / Jia, D.X. / Wang, A.H.-J. / Guo, R.T. ...Yang, Y. / Ko, T.P. / Li, J.H. / Liu, L. / Huang, C.H. / Chan, H.C. / Ren, F.F. / Jia, D.X. / Wang, A.H.-J. / Guo, R.T. / Chen, J. / Du, G.C.
CitationJournal: Chembiochem / Year: 2014
Title: Structural insights into enzymatic degradation of oxidized polyvinyl alcohol
Authors: Yang, Y. / Ko, T.P. / Liu, L. / Li, J. / Huang, C.H. / Chan, H.C. / Ren, F. / Jia, D. / Wang, A.H.-J. / Guo, R.T. / Chen, J. / Du, G.
History
DepositionNov 7, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxidized polyvinyl alcohol hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5212
Polymers39,3291
Non-polymers1921
Water7,422412
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.537, 65.426, 84.195
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Oxidized polyvinyl alcohol hydrolase / OPH / Oxidized PVA hydrolase / Beta-diketone hydrolase


Mass: 39328.789 Da / Num. of mol.: 1 / Fragment: UNP residues 30-379 / Mutation: S172C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: VM15C / Gene: pvaB / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LCQ7, beta-diketone hydrolase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.05 Å3/Da / Density % sol: 39.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M tri-sodium citrate, pH 5.6, 27% w/v Polyethylene Glycol 4000, 2% w/v n-Octyl-beta-D-glucoside, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2013
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. all: 43360 / Num. obs: 42894 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 35.9
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.4 / Num. unique all: 4007 / % possible all: 94.3

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
OASISmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
OASISphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→25 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.187 2110 RANDOM
Rwork0.159 --
all0.161 43360 -
obs0.161 42139 -
Solvent computationBsol: 37.6218 Å2
Displacement parametersBiso max: 50.07 Å2 / Biso mean: 16.5525 Å2 / Biso min: 7.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.316 Å20 Å20 Å2
2--4.036 Å20 Å2
3----4.351 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.08 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2596 0 13 412 3021
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.87
X-RAY DIFFRACTIONc_mcbond_it1.1641.5
X-RAY DIFFRACTIONc_scbond_it1.9752
X-RAY DIFFRACTIONc_mcangle_it1.6512
X-RAY DIFFRACTIONc_scangle_it2.8432.5
LS refinement shellResolution: 1.6→1.66 Å
RfactorNum. reflection
Rfree0.228 211
Rwork0.206 -
obs-3693
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4sulfon.param
X-RAY DIFFRACTION5ligand.param

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