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- PDB-3wla: Crystal Structure of sOPH Native -

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Basic information

Entry
Database: PDB / ID: 3wla
TitleCrystal Structure of sOPH 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 / periplasmic space
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
Oxidized polyvinyl alcohol hydrolase
Similarity search - Component
Biological speciesSphingopyxis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.3Nov 20, 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
C: Oxidized polyvinyl alcohol hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,0027
Polymers109,6173
Non-polymers3844
Water15,025834
1
A: Oxidized polyvinyl alcohol hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6352
Polymers36,5391
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxidized polyvinyl alcohol hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6352
Polymers36,5391
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Oxidized polyvinyl alcohol hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7313
Polymers36,5391
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.340, 75.742, 75.980
Angle α, β, γ (deg.)74.04, 88.67, 74.01
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: 36539.090 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingopyxis (bacteria) / Strain: 113P3 / Gene: oph / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q588Z2, beta-diketone hydrolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 834 / 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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Li2SO4, 0.1 M Bis-Tris pH 6.5, 3% v/v Polyethylene Glycol 500, 6% v/v Polyethylene Glycol 600, 25% w/v Polyethylene Glycol 3350, 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 13, 2012
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. all: 94534 / Num. obs: 92945 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 26.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.9 / Num. unique all: 9105 / % possible all: 96.5

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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 3WL5

3wl5


Resolution: 1.9→25 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.239 4475 RANDOM
Rwork0.193 --
all0.195 94534 -
obs0.195 88575 -
Solvent computationBsol: 60.8844 Å2
Displacement parametersBiso max: 90.15 Å2 / Biso mean: 31.9859 Å2 / Biso min: 14.22 Å2
Baniso -1Baniso -2Baniso -3
1-2.301 Å23.553 Å24.378 Å2
2---2.719 Å21.631 Å2
3---0.418 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7542 0 20 834 8396
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.84
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection
Rfree0.335 405
Rwork0.299 -
obs-7876

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