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- PDB-3wl6: Crystal Structure of pOPH Native -

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Basic information

Entry
Database: PDB / ID: 3wl6
TitleCrystal Structure of pOPH Native
ComponentsOxidized polyvinyl alcohol hydrolase
KeywordsHYDROLASE / alpha/beta-hydrolase / oxi-polyvinyl alcohol hydrolase
Function / homology
Function and homology information


beta-diketone hydrolase / beta-diketone hydrolase activity
Similarity search - Function
: / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Oxidized polyvinyl alcohol hydrolase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 8, 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
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxidized polyvinyl alcohol hydrolase
B: Oxidized polyvinyl alcohol hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7223
Polymers78,5292
Non-polymers1921
Water18,8981049
1
A: Oxidized polyvinyl alcohol hydrolase


Theoretical massNumber of molelcules
Total (without water)39,2651
Polymers39,2651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Oxidized polyvinyl alcohol hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4572
Polymers39,2651
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.934, 58.285, 65.350
Angle α, β, γ (deg.)89.63, 73.17, 75.76
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 39264.727 Da / Num. of mol.: 2 / Fragment: UNP residues 30-379
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.: 1049 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M tri-sodium citrate, pH 5.6, 29% w/v Polyethylene Glycol 4000, 3% 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: May 2, 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: 89981 / Num. obs: 85743 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.1
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.5 / Num. unique all: 8502 / % possible all: 94.3

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Processing

Software
NameVersionClassification
Blu-IceIcedata collection
PHASERphasing
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3WL5

3wl5


Resolution: 1.6→25 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.174 4254 RANDOM
Rwork0.152 --
all0.153 89981 -
obs0.153 83750 -
Solvent computationBsol: 41.3284 Å2
Displacement parametersBiso max: 59.41 Å2 / Biso mean: 19.441 Å2 / Biso min: 7.45 Å2
Baniso -1Baniso -2Baniso -3
1--7.823 Å25.138 Å20.106 Å2
2--2.875 Å2-1.381 Å2
3---4.948 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5002 0 13 1049 6064
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.62
X-RAY DIFFRACTIONc_mcbond_it1.1341.5
X-RAY DIFFRACTIONc_scbond_it2.0322
X-RAY DIFFRACTIONc_mcangle_it1.6852
X-RAY DIFFRACTIONc_scangle_it2.8942.5
LS refinement shellResolution: 1.6→1.66 Å
RfactorNum. reflection
Rfree0.224 446
Rwork0.209 -
obs-7572

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