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- PDB-5iq0: Crystal structure of Esterase mutant - F72G -

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Basic information

Entry
Database: PDB / ID: 5iq0
TitleCrystal structure of Esterase mutant - F72G
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: 1.799 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 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)152,9954
Polymers152,9954
Non-polymers00
Water17,042946
1
A: Esterase
B: Esterase


Theoretical massNumber of molelcules
Total (without water)76,4982
Polymers76,4982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-14 kcal/mol
Surface area23850 Å2
MethodPISA
2
C: Esterase
D: Esterase


Theoretical massNumber of molelcules
Total (without water)76,4982
Polymers76,4982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-9 kcal/mol
Surface area23980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.248, 95.637, 99.135
Angle α, β, γ (deg.)90.00, 95.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Esterase


Mass: 38248.785 Da / Num. of mol.: 4 / Mutation: F72G
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.: 946 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 59.36 %
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: Mar 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.799→36.17 Å / Num. obs: 167878 / % possible obs: 97.9 % / Redundancy: 5.6 % / Net I/σ(I): 44.86

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JKM

1jkm


Resolution: 1.799→36.167 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1973 2000 1.19 %
Rwork0.1754 --
obs0.1757 167868 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.799→36.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10569 0 0 946 11515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710817
X-RAY DIFFRACTIONf_angle_d1.02314767
X-RAY DIFFRACTIONf_dihedral_angle_d12.326443
X-RAY DIFFRACTIONf_chiral_restr0.061656
X-RAY DIFFRACTIONf_plane_restr0.0071958
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7991-1.84410.2641400.223811682X-RAY DIFFRACTION98
1.8441-1.8940.21011430.212211860X-RAY DIFFRACTION100
1.894-1.94970.22681450.20111930X-RAY DIFFRACTION100
1.9497-2.01260.23041430.196911846X-RAY DIFFRACTION100
2.0126-2.08460.1951430.194611857X-RAY DIFFRACTION100
2.0846-2.1680.21011430.186411899X-RAY DIFFRACTION100
2.168-2.26670.19981440.183911895X-RAY DIFFRACTION100
2.2667-2.38610.19961420.178311887X-RAY DIFFRACTION100
2.3861-2.53560.19741440.189211903X-RAY DIFFRACTION100
2.5356-2.73130.23481440.188811907X-RAY DIFFRACTION100
2.7313-3.00610.21641440.19311960X-RAY DIFFRACTION100
3.0061-3.44080.18441440.168711915X-RAY DIFFRACTION100
3.4408-4.33380.16641430.14611893X-RAY DIFFRACTION99
4.3338-36.17430.18751380.162911434X-RAY DIFFRACTION94

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