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- PDB-4ou4: Crystal structure of esterase rPPE mutant S159A complexed with (S... -

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Basic information

Entry
Database: PDB / ID: 4ou4
TitleCrystal structure of esterase rPPE mutant S159A complexed with (S)-Ac-CPA
ComponentsAlpha/beta hydrolase fold-3 domain protein
KeywordsHYDROLASE / A/B HYDROLASE FOLD / ESterase / HSL-like family
Function / homology
Function and homology information


Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / : / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2S)-(acetyloxy)(2-chlorophenyl)ethanoic acid / Alpha/beta hydrolase fold-3 domain protein
Similarity search - Component
Biological speciesPseudomonas (RNA similarity group I)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDou, S. / Kong, X.D. / Ma, B.D. / Xu, J.H. / Zhou, J.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Crystal structures of Pseudomonas putida esterase reveal the functional role of residues 187 and 287 in substrate binding and chiral recognition
Authors: Dou, S. / Kong, X.D. / Ma, B.D. / Chen, Q. / Zhang, J. / Zhou, J.H. / Xu, J.H.
History
DepositionFeb 15, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 30, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha/beta hydrolase fold-3 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7612
Polymers36,5321
Non-polymers2291
Water1,76598
1
A: Alpha/beta hydrolase fold-3 domain protein
hetero molecules

A: Alpha/beta hydrolase fold-3 domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5224
Polymers73,0652
Non-polymers4572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Unit cell
Length a, b, c (Å)94.624, 94.624, 88.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-583-

HOH

21A-585-

HOH

31A-590-

HOH

41A-595-

HOH

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Components

#1: Protein Alpha/beta hydrolase fold-3 domain protein / Esterase


Mass: 36532.320 Da / Num. of mol.: 1 / Mutation: S159A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas (RNA similarity group I) / Strain: ECU1011 / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: L7PYQ2, carboxylesterase
#2: Chemical ChemComp-S2T / (2S)-(acetyloxy)(2-chlorophenyl)ethanoic acid


Mass: 228.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9ClO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATED THE SEQUENCE DATABASE WAS WRONG AT THIS POSITION. RESIDUE 10 SHOULD BE GLN.

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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: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 16% (w/v) PEG8000, 0.04M KH2PO4, 20% glycerol, pH 7.5, 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: Dec 13, 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: 2.4→50 Å / Num. obs: 16307 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 33.19 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 6.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.498.70.81100
2.49-2.598.70.6721100
2.59-2.78.80.5651100
2.7-2.858.80.4551100
2.85-3.028.70.3431100
3.02-3.268.80.2461100
3.26-3.588.70.1711100
3.58-4.18.70.1151100
4.1-5.178.60.077199.9
5.17-5080.07199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YH2

2yh2


Resolution: 2.4→42.317 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 819 5.04 %
Rwork0.1672 --
obs0.1704 16258 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.49 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 15 98 2539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082518
X-RAY DIFFRACTIONf_angle_d1.1223426
X-RAY DIFFRACTIONf_dihedral_angle_d14.064907
X-RAY DIFFRACTIONf_chiral_restr0.042380
X-RAY DIFFRACTIONf_plane_restr0.006449
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.399-2.54930.26191480.1873248999
2.5493-2.74610.2561280.17962512100
2.7461-3.02240.27431480.17612537100
3.0224-3.45950.22831440.16292545100
3.4595-4.3580.21451270.15932598100
4.358-42.32370.22031240.1642758100

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