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- PDB-4o98: Crystal structure of Pseudomonas oleovorans PoOPH mutant H250I/I263W -

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Basic information

Entry
Database: PDB / ID: 4o98
TitleCrystal structure of Pseudomonas oleovorans PoOPH mutant H250I/I263W
Componentsorganophosphorus hydrolase
KeywordsHYDROLASE / alphabeta/betaalpha sandwich / organophophorus hydrolase / beta-lactamase superfamily / Zinc binding
Function / homology
Function and homology information


: / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Organophosphorus hydrolase
Similarity search - Component
Biological speciesPseudomonas oleovorans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.251 Å
AuthorsLuo, X.J. / Kong, X.D. / Zhao, J. / Chen, Q. / Zhou, J.H. / Xu, J.H.
CitationJournal: Biotechnol.Bioeng. / Year: 2014
Title: Switching a newly discovered lactonase into an efficient and thermostable phosphotriesterase by simple double mutations His250Ile/Ile263Trp
Authors: Luo, X.J. / Kong, X.D. / Zhao, J. / Chen, Q. / Zhou, J. / Xu, J.H.
History
DepositionJan 2, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: organophosphorus hydrolase
B: organophosphorus hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3516
Polymers73,0892
Non-polymers2624
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-171 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.742, 116.742, 83.395
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein organophosphorus hydrolase


Mass: 36544.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas oleovorans (bacteria) / Strain: DSMZ 50188 / Gene: OPHC / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0B4J186*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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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: 45.2 % / Mosaicity: 0.621 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.1M bicine/Trizma base, pH 8.3, 0.03M sodium fluoride, 0.03M sodium bromide, 0.03M sodium iodide, 12.5%(w/v) PEG1000, 12.5%(w/v) PEG3350, 12.5(v/v) (RS)-2-methyl-2,4-pentanediol., VAPOR ...Details: 0.1M bicine/Trizma base, pH 8.3, 0.03M sodium fluoride, 0.03M sodium bromide, 0.03M sodium iodide, 12.5%(w/v) PEG1000, 12.5%(w/v) PEG3350, 12.5(v/v) (RS)-2-methyl-2,4-pentanediol., VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 22, 2013
RadiationMonochromator: VARIMAX-HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 30699 / % possible obs: 99.5 % / Redundancy: 13.4 % / Biso Wilson estimate: 37.3 Å2 / Rmerge(I) obs: 0.055 / Χ2: 1.032 / Net I/σ(I): 26
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.3312.70.30329121.1195.1
2.33-2.4213.10.24530831.0141100
2.42-2.5313.30.19430741.0031100
2.53-2.6713.40.14430591.0061100
2.67-2.8313.50.11330621.0091100
2.83-3.0513.60.08530871.0091100
3.05-3.3613.70.06530701.0961100
3.36-3.8513.70.04930831.031100
3.85-4.8513.60.03831130.99199.9
4.85-5013.40.03131561.0691100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.251→43.229 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8422 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 22.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2195 1548 5.05 %
Rwork0.1774 --
obs0.1796 30662 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.58 Å2 / Biso mean: 41.6621 Å2 / Biso min: 24.31 Å2
Refinement stepCycle: LAST / Resolution: 2.251→43.229 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4678 0 4 204 4886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084795
X-RAY DIFFRACTIONf_angle_d1.2636531
X-RAY DIFFRACTIONf_chiral_restr0.087723
X-RAY DIFFRACTIONf_plane_restr0.006858
X-RAY DIFFRACTIONf_dihedral_angle_d15.8191723
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2515-2.32420.26231420.18912608275099
2.3242-2.40720.29491470.200126242771100
2.4072-2.50360.26651420.226092751100
2.5036-2.61750.26461290.193926692798100
2.6175-2.75550.2481450.18926342779100
2.7555-2.92810.281480.19926412789100
2.9281-3.15410.27371390.199626402779100
3.1541-3.47140.21231430.179826442787100
3.4714-3.97340.18211460.165326612807100
3.9734-5.00490.18881320.152126602792100
5.0049-43.23690.18011350.174127242859100

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