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- PDB-2c7b: The Crystal Structure of EstE1, a New Thermophilic and Thermostab... -

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Basic information

Entry
Database: PDB / ID: 2c7b
TitleThe Crystal Structure of EstE1, a New Thermophilic and Thermostable Carboxylesterase Cloned from a Metagenomic Library
ComponentsCARBOXYLESTERASE
KeywordsHYDROLASE / CARBOXYESTERASE / THERMOPHILIC ENZYME / HSL / ALPHA/BETA HYDROLASE FOLD
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity
Similarity search - Function
Lipase, GDXG, putative serine active site / Lipolytic enzymes "G-D-X-G" family, putative serine 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
Biological speciesUNCULTURED ARCHAEON (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsByun, J.-S. / Rhee, J.-K. / Kim, D.-U. / Oh, J.-W. / Cho, H.-S.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: Crystal Structure of Hyperthermophilic Esterase Este1 and the Relationship between its Dimerization and Thermostability Properties.
Authors: Byun, J.-S. / Rhee, J.-K. / Kim, N.D. / Yoon, J. / Kim, D.-U. / Koh, E. / Oh, J.-W. / Cho, H.-S.
History
DepositionNov 21, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBOXYLESTERASE
B: CARBOXYLESTERASE


Theoretical massNumber of molelcules
Total (without water)68,1162
Polymers68,1162
Non-polymers00
Water2,486138
1
A: CARBOXYLESTERASE
B: CARBOXYLESTERASE

A: CARBOXYLESTERASE
B: CARBOXYLESTERASE


Theoretical massNumber of molelcules
Total (without water)136,2334
Polymers136,2334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)73.710, 73.710, 234.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CARBOXYLESTERASE / ESTE1


Mass: 34058.164 Da / Num. of mol.: 2 / Fragment: ALPHA-BETA HYDROLASE FOLD, RESIDUES 1-311
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) UNCULTURED ARCHAEON (environmental samples)
Description: METAGENOMES FROM THERMAL ENVIRONMENTAL SAMPLES / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5G935, carboxylesterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.47 Å3/Da / Density % sol: 49.74 %
Crystal growpH: 7.5
Details: 0.1M BIS-TRIS PH6.5, 0.2M AMMONIUM SULFATE, 35%(W/V) PEG 3350, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 1
DetectorType: BRUKER AXS / Detector: CCD / Date: Jul 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 29848 / % possible obs: 99.8 % / Observed criterion σ(I): 4.1 / Redundancy: 2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.6
Reflection shellResolution: 2.3→2.6 Å / Mean I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2613 2721 3.8 %RANDOM
Rwork0.2338 ---
obs0.2338 54674 76.1 %-
Solvent computationBsol: 40.3777 Å2 / ksol: 0.363934 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.777 Å20 Å20 Å2
2---2.777 Å20 Å2
3---5.554 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4469 0 0 138 4607
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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