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- PDB-5gmr: Crystal structure of the mutant M3+S202W/I203F of the esterase E40 -

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Basic information

Entry
Database: PDB / ID: 5gmr
TitleCrystal structure of the mutant M3+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: 1.8 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
C: Esterase
A: Esterase
B: Esterase
D: Esterase


Theoretical massNumber of molelcules
Total (without water)137,2564
Polymers137,2564
Non-polymers00
Water23,8701325
1
C: Esterase


Theoretical massNumber of molelcules
Total (without water)34,3141
Polymers34,3141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Esterase


Theoretical massNumber of molelcules
Total (without water)34,3141
Polymers34,3141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Esterase


Theoretical massNumber of molelcules
Total (without water)34,3141
Polymers34,3141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Esterase


Theoretical massNumber of molelcules
Total (without water)34,3141
Polymers34,3141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.133, 73.679, 85.553
Angle α, β, γ (deg.)67.54, 68.32, 76.86
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Esterase / Esterase E40


Mass: 34314.117 Da / Num. of mol.: 4
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.: 1325 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES ARG22-LYS23-THR24 OF E40 (UNIPROTKB - A0A0F6WGE1 (A0A0F6WGE1_9BACT)) WERE REPLACED BY ...RESIDUES ARG22-LYS23-THR24 OF E40 (UNIPROTKB - A0A0F6WGE1 (A0A0F6WGE1_9BACT)) WERE REPLACED BY RESIDUES TYR22-LYS23-HIS24-LEU25-SER26 TO GENERATE THE MUTANT M3.

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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: 2.48 Å3/Da / Density % sol: 50.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M succinic acid (pH 6.5), 15% (w/v) PEG 3350

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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: 1.8→50 Å / Num. obs: 118334 / % possible obs: 96.6 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.613
Reflection shellResolution: 1.8→1.86 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: 1.8→40.007 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 24.39
RfactorNum. reflection% reflection
Rfree0.2041 5350 4.9 %
Rwork0.1677 --
obs0.1695 109130 88.64 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Bsol: 45.529 Å2 / ksol: 0.355 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7859 Å212.0668 Å21.981 Å2
2--6.3024 Å210.5226 Å2
3----7.0883 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9088 0 0 1325 10413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069340
X-RAY DIFFRACTIONf_angle_d0.99912738
X-RAY DIFFRACTIONf_dihedral_angle_d11.8493422
X-RAY DIFFRACTIONf_chiral_restr0.0671402
X-RAY DIFFRACTIONf_plane_restr0.0051674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.795-1.81540.29241150.25572374X-RAY DIFFRACTION61
1.8154-1.83680.30531460.25722852X-RAY DIFFRACTION74
1.8368-1.85920.32151550.25083019X-RAY DIFFRACTION75
1.8592-1.88270.27871420.23812969X-RAY DIFFRACTION78
1.8827-1.90750.26541710.22253108X-RAY DIFFRACTION79
1.9075-1.93360.2821630.21973101X-RAY DIFFRACTION80
1.9336-1.96120.23851670.20383167X-RAY DIFFRACTION82
1.9612-1.99050.24191750.20463243X-RAY DIFFRACTION82
1.9905-2.02160.26671830.19733272X-RAY DIFFRACTION85
2.0216-2.05480.23171760.20393388X-RAY DIFFRACTION86
2.0548-2.09020.24611880.17873405X-RAY DIFFRACTION87
2.0902-2.12820.22861780.18683412X-RAY DIFFRACTION88
2.1282-2.16910.23041870.17463472X-RAY DIFFRACTION89
2.1691-2.21340.21021920.15863510X-RAY DIFFRACTION90
2.2134-2.26150.20881590.16153601X-RAY DIFFRACTION92
2.2615-2.31410.19761740.16113557X-RAY DIFFRACTION91
2.3141-2.3720.22661820.15713658X-RAY DIFFRACTION93
2.372-2.43610.19711660.15553670X-RAY DIFFRACTION93
2.4361-2.50780.19731890.16443668X-RAY DIFFRACTION94
2.5078-2.58870.20371770.16053665X-RAY DIFFRACTION94
2.5887-2.68120.2042070.17083683X-RAY DIFFRACTION95
2.6812-2.78860.21652050.16123705X-RAY DIFFRACTION95
2.7886-2.91540.20281830.17093737X-RAY DIFFRACTION96
2.9154-3.06910.20951770.16823794X-RAY DIFFRACTION96
3.0691-3.26130.2071930.16733766X-RAY DIFFRACTION97
3.2613-3.5130.19551960.16583814X-RAY DIFFRACTION98
3.513-3.86620.18681940.15243816X-RAY DIFFRACTION97
3.8662-4.42510.16341900.143777X-RAY DIFFRACTION97
4.4251-5.57270.1542070.13953757X-RAY DIFFRACTION97
5.5727-40.01680.16822130.15143820X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 13.0197 Å / Origin y: -53.5512 Å / Origin z: -25.7925 Å
111213212223313233
T0.1562 Å2-0.0047 Å2-0.003 Å2-0.1572 Å2-0.003 Å2--0.1606 Å2
L0.0123 °2-0.0073 °2-0.0317 °2-0.0201 °20.0037 °2--0.0239 °2
S0.001 Å °0.0037 Å °-0.0076 Å °0.001 Å °-0.0008 Å °0.0017 Å °-0.0017 Å °-0.0028 Å °-0 Å °
Refinement TLS groupSelection details: all

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