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- PDB-3wwc: The complex of pOPH_S172A of pNPB -

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Basic information

Entry
Database: PDB / ID: 3wwc
TitleThe complex of pOPH_S172A of pNPB
ComponentsOxidized polyvinyl alcohol hydrolase
KeywordsHYDROLASE / tryptophan / disulfide bridge / p-nitrophenyl esters
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
butanoic acid / CITRIC ACID / Oxidized polyvinyl alcohol hydrolase
Similarity search - Component
Biological speciesPseudomonas sp. VM15C (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsYang, Y. / Ko, T.P. / Li, J.H. / Liu, L. / Huang, C.H. / Chen, J. / Guo, R.T. / Du, G.C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Roles of tryptophan residue and disulfide bond in the variable lid region of oxidized polyvinyl alcohol hydrolase
Authors: Yang, Y. / Ko, T.P. / Liu, L. / Li, J. / Huang, C.H. / Chen, J. / Guo, R.T. / Du, G.
History
DepositionJun 17, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidized polyvinyl alcohol hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6174
Polymers39,2491
Non-polymers3683
Water10,016556
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.326, 65.236, 84.334
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: 39248.727 Da / Num. of mol.: 1 / Fragment: UNP residues 30-379 / Mutation: S172A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. VM15C (bacteria) / Gene: pvaB / Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: Chemical ChemComp-BUA / butanoic acid


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.04 Å3/Da / Density % sol: 39.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M tri-sodium citrate, pH 5.6, 30% w/v Polyethylene Glycol 4000, 0.3% 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: Sep 13, 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: 1.49→25 Å / Num. all: 53249 / Num. obs: 52709 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 24.6
Reflection shellResolution: 1.49→1.54 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 3 / Num. unique all: 5167 / % possible all: 99.5

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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 3WL6

3wl6


Resolution: 1.49→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.173 2546 RANDOM
Rwork0.154 --
all0.155 53249 -
obs0.155 50987 -
Solvent computationBsol: 42.3899 Å2
Displacement parametersBiso mean: 17.8032 Å2
Baniso -1Baniso -2Baniso -3
1-1.627 Å20 Å20 Å2
2--1.577 Å20 Å2
3----3.204 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.1 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.49→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 25 556 3151
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.79
X-RAY DIFFRACTIONc_mcbond_it1.1561.5
X-RAY DIFFRACTIONc_scbond_it2.0312
X-RAY DIFFRACTIONc_mcangle_it1.7662
X-RAY DIFFRACTIONc_scangle_it2.9242.5
LS refinement shellResolution: 1.49→1.54 Å
RfactorNum. reflection
Rfree0.259 203
Rwork0.232 -
obs-4295
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2butyl_acid.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4citrate_acid.param

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