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- PDB-5iq3: Crystal structure of Esterase mutant - F72G/L255W -

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Basic information

Entry
Database: PDB / ID: 5iq3
TitleCrystal structure of Esterase mutant - F72G/L255W
ComponentsEsterase
KeywordsHYDROLASE / Esterase / Est25 / Hormone-Sensitive Lipase
Function / homology
Function and homology information


: / 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 bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSeok, S.-H. / Seo, M.-D. / Kim, J. / Ryu, Y.
CitationJournal: To Be Published
Title: Crystal structure of Esterase mutant - F72G
Authors: Seok, S.-H. / Seo, M.-D. / Kim, J. / Ryu, Y.
History
DepositionMar 10, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Esterase
B: Esterase
C: Esterase
D: Esterase


Theoretical massNumber of molelcules
Total (without water)153,2874
Polymers153,2874
Non-polymers00
Water21,6901204
1
A: Esterase
B: Esterase


Theoretical massNumber of molelcules
Total (without water)76,6442
Polymers76,6442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-13 kcal/mol
Surface area23620 Å2
MethodPISA
2
C: Esterase
D: Esterase


Theoretical massNumber of molelcules
Total (without water)76,6442
Polymers76,6442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-7 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.521, 95.877, 98.527
Angle α, β, γ (deg.)90.00, 95.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-406-

HOH

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Components

#1: Protein
Esterase


Mass: 38321.836 Da / Num. of mol.: 4 / Mutation: F72G,L255W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: Q4TZQ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1204 / 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: 3 Å3/Da / Density % sol: 58.98 %
Crystal growTemperature: 299 K / Method: microbatch / pH: 7 / Details: 2.4 M sodium malonate (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00004 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.75→25.36 Å / Num. obs: 182179 / % possible obs: 99.9 % / Redundancy: 6.2 % / Net I/σ(I): 33.67
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 4.63 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
PHENIX1.10.1_2155refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→25.36 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.88
RfactorNum. reflection% reflection
Rfree0.1832 2000 1.1 %
Rwork0.1688 --
obs0.169 182176 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→25.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10569 0 0 1204 11773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110776
X-RAY DIFFRACTIONf_angle_d1.10914716
X-RAY DIFFRACTIONf_dihedral_angle_d11.9436396
X-RAY DIFFRACTIONf_chiral_restr0.0651640
X-RAY DIFFRACTIONf_plane_restr0.0071948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7478-1.79150.26451380.237212456X-RAY DIFFRACTION97
1.7915-1.83990.24961430.218712848X-RAY DIFFRACTION100
1.8399-1.8940.22961430.203612882X-RAY DIFFRACTION100
1.894-1.95510.21311420.192412841X-RAY DIFFRACTION100
1.9551-2.0250.22911430.188812847X-RAY DIFFRACTION100
2.025-2.1060.23491430.182512879X-RAY DIFFRACTION100
2.106-2.20180.17561430.174112885X-RAY DIFFRACTION100
2.2018-2.31780.19841430.172212896X-RAY DIFFRACTION100
2.3178-2.46290.20861430.17612910X-RAY DIFFRACTION100
2.4629-2.65290.21111430.181312893X-RAY DIFFRACTION100
2.6529-2.91950.1641440.18712892X-RAY DIFFRACTION100
2.9195-3.34120.16691440.165812943X-RAY DIFFRACTION100
3.3412-4.20650.15521430.137812974X-RAY DIFFRACTION100
4.2065-25.5150.16081450.152213030X-RAY DIFFRACTION99

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