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- PDB-5iq2: Crystal structure of Esterase mutant - L255W -

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Basic information

Entry
Database: PDB / ID: 5iq2
TitleCrystal structure of Esterase mutant - 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: 1.78 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)153,6484
Polymers153,6484
Non-polymers00
Water22,9331273
1
A: Esterase
B: Esterase


Theoretical massNumber of molelcules
Total (without water)76,8242
Polymers76,8242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-12 kcal/mol
Surface area23710 Å2
MethodPISA
2
C: Esterase
D: Esterase


Theoretical massNumber of molelcules
Total (without water)76,8242
Polymers76,8242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-9 kcal/mol
Surface area23690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.458, 95.454, 99.266
Angle α, β, γ (deg.)90.00, 96.58, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-677-

HOH

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Components

#1: Protein
Esterase


Mass: 38411.957 Da / Num. of mol.: 4 / Mutation: 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.: 1273 / 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: 3.01 Å3/Da / Density % sol: 59.12 %
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: 0.97935 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.78→25 Å / Num. obs: 174151 / % possible obs: 100 % / Redundancy: 7.5 % / Net I/σ(I): 38.83
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 6.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→22.725 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1956 2000 1.15 %
Rwork0.1724 --
obs0.1726 174014 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→22.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10585 0 0 1273 11858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810845
X-RAY DIFFRACTIONf_angle_d1.08614811
X-RAY DIFFRACTIONf_dihedral_angle_d12.3926435
X-RAY DIFFRACTIONf_chiral_restr0.0651651
X-RAY DIFFRACTIONf_plane_restr0.0071959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7795-1.8240.25881410.221212141X-RAY DIFFRACTION99
1.824-1.87330.22521420.20412262X-RAY DIFFRACTION100
1.8733-1.92840.21951420.200512199X-RAY DIFFRACTION100
1.9284-1.99060.23571430.194112312X-RAY DIFFRACTION100
1.9906-2.06170.2131430.189312265X-RAY DIFFRACTION100
2.0617-2.14420.21091420.185412225X-RAY DIFFRACTION100
2.1442-2.24170.22941430.181312221X-RAY DIFFRACTION100
2.2417-2.35980.19461420.178812299X-RAY DIFFRACTION100
2.3598-2.50740.21430.187912286X-RAY DIFFRACTION100
2.5074-2.70070.22231430.189412312X-RAY DIFFRACTION100
2.7007-2.9720.21741430.191912299X-RAY DIFFRACTION100
2.972-3.40080.21761440.16912325X-RAY DIFFRACTION100
3.4008-4.280.1531430.139412356X-RAY DIFFRACTION100
4.28-22.72680.15081460.144712512X-RAY DIFFRACTION100

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