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- PDB-1zoi: Crystal Structure of a Stereoselective Esterase from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 1zoi
TitleCrystal Structure of a Stereoselective Esterase from Pseudomonas putida IFO12996
Componentsesterase
KeywordsHYDROLASE / Esterase / Pseudomonas putida / alpha/beta hydrolase fold
Function / homology: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Esterase
Function and homology information
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsElmi, F. / Lee, H.T. / Huang, J.Y. / Hsieh, Y.C. / Wang, Y.L. / Chen, Y.J. / Shaw, S.Y. / Chen, C.J.
CitationJournal: J.Bacteriol. / Year: 2005
Title: Stereoselective esterase from Pseudomonas putida IFO12996 reveals alpha/beta hydrolase folds for D-beta-acetylthioisobutyric acid synthesis
Authors: Elmi, F. / Lee, H.T. / Huang, J.Y. / Hsieh, Y.C. / Wang, Y.L. / Chen, Y.J. / Shaw, S.Y. / Chen, C.J.
History
DepositionMay 13, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: esterase
B: esterase
C: esterase


Theoretical massNumber of molelcules
Total (without water)90,6063
Polymers90,6063
Non-polymers00
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-24 kcal/mol
Surface area27470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.556, 98.108, 153.63
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a homotrimer.

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Components

#1: Protein esterase


Mass: 30201.867 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q3HWU8, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O

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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: 2.091 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: ammonium sulphate, citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 2004
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. all: 97023 / Num. obs: 93768 / % possible obs: 92.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 %
Reflection shellResolution: 1.6→1.66 Å / % possible all: 82.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALAdata scaling
CNSrefinement
HKL-2000data reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.239 9413 RANDOM
Rwork0.22 --
all0.223 97023 -
obs0.22 93768 -
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6377 0 0 317 6694
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.302
X-RAY DIFFRACTIONc_dihedral_angle_deg23.117
X-RAY DIFFRACTIONc_improper_angle_deg0.851

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