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- PDB-4ob6: Complex structure of esterase rPPE S159A/W187H and substrate (S)-... -

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Basic information

Entry
Database: PDB / ID: 4ob6
TitleComplex structure of esterase rPPE S159A/W187H and substrate (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: 1.7 Å
AuthorsDou, S. / Kong, X.D. / Ma, B.D. / Chen, Q. / Zhou, J.H. / Xu, 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
DepositionJan 7, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,4994
Polymers36,8141
Non-polymers6863
Water4,017223
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)74,9998
Polymers73,6272
Non-polymers1,3726
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)95.438, 95.438, 88.297
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-545-

HOH

21A-549-

HOH

31A-561-

HOH

41A-637-

HOH

51A-686-

HOH

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Components

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


Mass: 36813.602 Da / Num. of mol.: 1 / Mutation: S159A/W187H
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, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-S2T / (2S)-(acetyloxy)(2-chlorophenyl)ethanoic acid


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


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATED THE SEQUENCE DATABASE WAS WRONG AT THIS POSITION.

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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: 2.73 Å3/Da / Density % sol: 54.96 % / Mosaicity: 0.528 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 16% (w/v) PEG 8000, 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: Oct 30, 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: 1.7→33.742 Å / Num. obs: 45435 / % possible obs: 100 % / Redundancy: 16.7 % / Biso Wilson estimate: 21.32 Å2 / Rmerge(I) obs: 0.067 / Χ2: 1.066 / Net I/σ(I): 16.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.7616.20.41244621.0841100
1.76-1.8316.40.29844801.0761100
1.83-1.9116.40.22644491.0971100
1.91-2.0216.60.17344791.0931100
2.02-2.1416.70.13244971.0411100
2.14-2.3116.90.10745161.0341100
2.31-2.54170.08845411.0051100
2.54-2.9117.10.07345521.1011100
2.91-3.6617.10.05646191.071100
3.66-5016.60.04248401.059199.8

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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
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YH2

2yh2


Resolution: 1.7→33.742 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.9009 / SU ML: 0.16 / σ(F): 1.34 / Phase error: 15.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1812 2280 5.03 %
Rwork0.1644 --
obs0.1652 45369 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.67 Å2 / Biso mean: 22.5086 Å2 / Biso min: 13.63 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.742 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2422 0 45 223 2690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072538
X-RAY DIFFRACTIONf_angle_d1.1913451
X-RAY DIFFRACTIONf_chiral_restr0.085382
X-RAY DIFFRACTIONf_plane_restr0.005451
X-RAY DIFFRACTIONf_dihedral_angle_d13.107912
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7002-1.73720.26191430.201726512794
1.7372-1.77760.21271450.172826392784
1.7776-1.82210.19641470.149326242771
1.8221-1.87130.20011370.1526732810
1.8713-1.92640.19111400.150826382778
1.9264-1.98860.1831430.155826802823
1.9886-2.05960.17481390.155326562795
2.0596-2.14210.17581530.158126442797
2.1421-2.23950.17771390.157826882827
2.2395-2.35760.18481400.163326752815
2.3576-2.50530.19851490.1726852834
2.5053-2.69860.20251270.172627092836
2.6986-2.970.20081440.174827092853
2.97-3.39950.18881590.173927202879
3.3995-4.28160.15171390.15727642903
4.2816-33.74910.16111360.163229343070

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