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- PDB-3wwd: The complex of pOPH_S172C with DMSO -

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Basic information

Entry
Database: PDB / ID: 3wwd
TitleThe complex of pOPH_S172C with DMSO
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
CITRIC ACID / Oxidized polyvinyl alcohol hydrolase
Similarity search - Component
Biological speciesPseudomonas sp. VM15C (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)39,5993
Polymers39,3291
Non-polymers2702
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.516, 65.281, 84.167
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. 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: Jul 8, 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: 1.65→25 Å / Num. all: 39487 / Num. obs: 39500 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 23.6
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 6 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 4.8 / Num. unique all: 3895 / % possible all: 100

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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: 1.65→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.193 1919 RANDOM
Rwork0.167 --
all0.168 39487 -
obs0.168 38410 -
Solvent computationBsol: 32.7169 Å2
Displacement parametersBiso mean: 13.4557 Å2
Baniso -1Baniso -2Baniso -3
1-1.545 Å20 Å20 Å2
2--0.63 Å20 Å2
3----2.175 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.65→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 17 524 3121
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0045
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_mcbond_it0.9231.5
X-RAY DIFFRACTIONc_scbond_it1.7142
X-RAY DIFFRACTIONc_mcangle_it1.3772
X-RAY DIFFRACTIONc_scangle_it2.4792.5
LS refinement shellResolution: 1.65→1.71 Å
RfactorNum. reflection
Rfree0.222 185
Rwork0.208 -
obs-3610
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3sulfon.param
X-RAY DIFFRACTION4ligand2.param

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