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- PDB-1aur: PMSF-INHIBITED CARBOXYLESTERASE FROM PSEUDOMONAS FLUORESCENS -

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Basic information

Entry
Database: PDB / ID: 1aur
TitlePMSF-INHIBITED CARBOXYLESTERASE FROM PSEUDOMONAS FLUORESCENS
ComponentsCARBOXYLESTERASE
KeywordsHYDROLASE
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity
Similarity search - Function
Phospholipase/carboxylesterase/thioesterase / Phospholipase/Carboxylesterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
phenylmethanesulfonic acid / Carboxylesterase 2
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsKim, K.K. / Song, H.K. / Suh, S.W.
CitationJournal: Structure / Year: 1997
Title: Crystal structure of carboxylesterase from Pseudomonas fluorescens, an alpha/beta hydrolase with broad substrate specificity.
Authors: Kim, K.K. / Song, H.K. / Shin, D.H. / Hwang, K.Y. / Choe, S. / Yoo, O.J. / Suh, S.W.
History
DepositionSep 1, 1997Processing site: BNL
Revision 1.0Mar 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBOXYLESTERASE
B: CARBOXYLESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1474
Polymers47,8022
Non-polymers3442
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.490, 81.490, 144.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.669442, -0.070588, 0.739503), (-0.010899, -0.996301, -0.085234), (0.742784, 0.048999, -0.667735)
Vector: -26.3075, 67.1341, 62.8966)

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Components

#1: Protein CARBOXYLESTERASE /


Mass: 23901.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: Q53547, carboxylesterase
#2: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Compound detailsACTIVE SERINE RESIDUE WAS COVALENTLY MODIFIED BY PMSF.

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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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.10 MHEPES1reservoir
21.4 Mammonium sulfate1reservoir
30.20 Mlithium sulfate1reservoir
44.0 %(v/v)dioxane1reservoir
50.10 Mn-propanol1drop
6PMSF inhibitor1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Mar 1, 1992
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→99 Å / Num. obs: 15245 / % possible obs: 88.5 % / Observed criterion σ(I): 1 / Redundancy: 8.2 % / Rmerge(I) obs: 0.043

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Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
PROCORdata reduction
FSSCALEdata scaling
X-PLOR3.843phasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.254 -10 %RANDOM
Rwork0.181 ---
obs0.181 15125 88.5 %-
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 20 199 3583
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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