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- PDB-5gms: Crystal structure of the mutant S202W/I203F of the esterase E40 -

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Basic information

Entry
Database: PDB / ID: 5gms
TitleCrystal structure of the mutant S202W/I203F of the esterase E40
ComponentsEsterase
KeywordsHYDROLASE / esterase
Function / homology
Function and homology information


Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine 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 bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhang, Y.-Z. / Li, P.-Y.
CitationJournal: Appl. Environ. Microbiol. / Year: 2017
Title: Structural and Mechanistic Insights into the Improvement of the Halotolerance of a Marine Microbial Esterase by Increasing Intra- and Interdomain Hydrophobic Interactions.
Authors: Li, P.Y. / Zhang, Y. / Xie, B.B. / Zhang, Y.Q. / Hao, J. / Wang, Y. / Wang, P. / Li, C.Y. / Qin, Q.L. / Zhang, X.Y. / Su, H.N. / Shi, M. / Zhang, Y.Z. / Chen, X.L.
History
DepositionJul 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Esterase
B: Esterase


Theoretical massNumber of molelcules
Total (without water)68,1422
Polymers68,1422
Non-polymers00
Water8,683482
1
A: Esterase


Theoretical massNumber of molelcules
Total (without water)34,0711
Polymers34,0711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Esterase


Theoretical massNumber of molelcules
Total (without water)34,0711
Polymers34,0711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.108, 144.845, 96.067
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Esterase / Esterase E40


Mass: 34070.859 Da / Num. of mol.: 2 / Mutation: S202W, I203F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0F6WGE1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M imidazole (pH 7.0), 50% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 69213 / % possible obs: 99.8 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 77.3
Reflection shellResolution: 1.7→1.76 Å

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
PHENIXmodel building
HKL-3000data scaling
SHELXDEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XVC

4xvc


Resolution: 1.7→42.557 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 16.5
RfactorNum. reflection% reflection
Rfree0.1796 3434 5.06 %
Rwork0.1619 --
obs0.1628 67899 98.1 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Bsol: 46.147 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.7364 Å2-0 Å20 Å2
2---3.9201 Å2-0 Å2
3---5.6565 Å2
Refinement stepCycle: LAST / Resolution: 1.7→42.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4534 0 0 482 5016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014668
X-RAY DIFFRACTIONf_angle_d1.4456370
X-RAY DIFFRACTIONf_dihedral_angle_d13.8761722
X-RAY DIFFRACTIONf_chiral_restr0.092706
X-RAY DIFFRACTIONf_plane_restr0.007838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7002-1.72350.18581060.18982492X-RAY DIFFRACTION95
1.7235-1.74810.25381190.18632528X-RAY DIFFRACTION96
1.7481-1.77420.20541310.17782512X-RAY DIFFRACTION96
1.7742-1.80190.19931360.18212512X-RAY DIFFRACTION97
1.8019-1.83140.1731320.16742513X-RAY DIFFRACTION97
1.8314-1.8630.19751440.16532521X-RAY DIFFRACTION97
1.863-1.89690.20581380.16392511X-RAY DIFFRACTION97
1.8969-1.93340.18521420.16052522X-RAY DIFFRACTION97
1.9334-1.97280.16241460.16352528X-RAY DIFFRACTION97
1.9728-2.01570.17071300.15822569X-RAY DIFFRACTION98
2.0157-2.06260.20531230.1592583X-RAY DIFFRACTION99
2.0626-2.11420.18351400.16162563X-RAY DIFFRACTION99
2.1142-2.17140.17751530.15712567X-RAY DIFFRACTION99
2.1714-2.23530.18051430.15442608X-RAY DIFFRACTION99
2.2353-2.30740.1791250.15542589X-RAY DIFFRACTION99
2.3074-2.38990.17891460.15512592X-RAY DIFFRACTION99
2.3899-2.48550.17221290.16042602X-RAY DIFFRACTION99
2.4855-2.59870.16441320.15662611X-RAY DIFFRACTION99
2.5987-2.73560.21251330.15762641X-RAY DIFFRACTION100
2.7356-2.9070.16531370.16342616X-RAY DIFFRACTION100
2.907-3.13140.19961420.16232639X-RAY DIFFRACTION100
3.1314-3.44640.16231350.15892652X-RAY DIFFRACTION100
3.4464-3.94480.16321440.14552658X-RAY DIFFRACTION100
3.9448-4.96880.15531720.15092660X-RAY DIFFRACTION100
4.9688-42.57080.20471560.19332676X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -18.8437 Å / Origin y: 16.5523 Å / Origin z: 18.0881 Å
111213212223313233
T0.0879 Å20.0134 Å2-0.0018 Å2-0.1278 Å2-0.0219 Å2--0.1107 Å2
L0.2861 °20.0347 °20.1679 °2-0.3218 °20.0897 °2--0.3423 °2
S-0.0147 Å °-0.0419 Å °0.0486 Å °-0.0004 Å °-0.0416 Å °0.053 Å °-0.0269 Å °-0.1138 Å °0.0548 Å °
Refinement TLS groupSelection details: all

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