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- PDB-4ou5: Crystal structure of esterase rPPE mutant S159A/W187H -

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Basic information

Entry
Database: PDB / ID: 4ou5
TitleCrystal structure of esterase rPPE mutant S159A/W187H
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
DI(HYDROXYETHYL)ETHER / Alpha/beta hydrolase fold-3 domain protein
Similarity search - Component
Biological speciesPseudomonas (RNA similarity group I)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.99 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 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)36,7093
Polymers36,4841
Non-polymers2242
Water6,702372
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)73,4176
Polymers72,9692
Non-polymers4494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)95.754, 95.754, 88.900
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-575-

HOH

21A-593-

HOH

31A-625-

HOH

41A-645-

HOH

51A-663-

HOH

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Components

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


Mass: 36484.258 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, carboxylesterase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes/Mops-Na, pH 7.5, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03M MgCl2, 0.03M CaCl2, 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
RadiationMonochromator: VARIMAX-HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 28983 / % possible obs: 99.9 % / Redundancy: 17.8 % / Biso Wilson estimate: 26.71 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.99-2.0617.20.8831100
2.06-2.1417.20.6851100
2.14-2.2417.30.521100
2.24-2.3617.30.3951100
2.36-2.5117.60.3031100
2.51-2.717.90.2311100
2.7-2.9718.30.1581100
2.97-3.418.60.1021100
3.4-4.2918.60.064199.9
4.29-5017.80.041199.7

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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: 1.99→38.58 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 15.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1778 1472 5.09 %
Rwork0.1399 --
obs0.1418 28928 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.66 Å2
Refinement stepCycle: LAST / Resolution: 1.99→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 15 372 2813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072501
X-RAY DIFFRACTIONf_angle_d1.0413395
X-RAY DIFFRACTIONf_dihedral_angle_d13.615907
X-RAY DIFFRACTIONf_chiral_restr0.043377
X-RAY DIFFRACTIONf_plane_restr0.005444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9904-2.05460.22041420.17642439
2.0546-2.1280.19681170.15922479
2.128-2.21320.18041280.14862449
2.2132-2.31390.23311330.14792440
2.3139-2.43590.1751310.14922470
2.4359-2.58850.1991600.14992444
2.5885-2.78830.20371260.15182495
2.7883-3.06880.20471460.14832477
3.0688-3.51260.17451300.13632516
3.5126-4.42450.15081320.12212542
4.4245-38.58720.14161270.12972705

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