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- PDB-7e16: crystal structure of GDSL esterase from Geobacillus thermodenitri... -

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Basic information

Entry
Database: PDB / ID: 7.0E+16
Titlecrystal structure of GDSL esterase from Geobacillus thermodenitrificans
ComponentsGDSL-family esterase
KeywordsHYDROLASE / esterase
Function / homology: / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / hydrolase activity, acting on ester bonds / phosphatidylcholine lysophospholipase activity / GDSL-family esterase
Function and homology information
Biological speciesGeobacillus thermodenitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsChen, L.
CitationJournal: To Be Published
Title: Rational engineering of substrate selectivity of GDSL esterase from Geobacillus thermodenitrificans
Authors: Zhang, Y.
History
DepositionJan 31, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: GDSL-family esterase
B: GDSL-family esterase


Theoretical massNumber of molelcules
Total (without water)58,6982
Polymers58,6982
Non-polymers00
Water36020
1
A: GDSL-family esterase


Theoretical massNumber of molelcules
Total (without water)29,3491
Polymers29,3491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GDSL-family esterase


Theoretical massNumber of molelcules
Total (without water)29,3491
Polymers29,3491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.424, 106.424, 128.643
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein GDSL-family esterase


Mass: 29348.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2ZAB3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.1 Å3/Da / Density % sol: 60.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jan 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 22907 / % possible obs: 99.2 % / Redundancy: 20 % / CC1/2: 0.968 / Rpim(I) all: 0.024 / Rrim(I) all: 0.118 / Net I/σ(I): 1.9
Reflection shellResolution: 2.6→2.64 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1126 / CC1/2: 0.933 / Rpim(I) all: 0.227 / Rsym value: 1.144

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U8U

1u8u


Resolution: 2.62→32.5 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.925 / SU B: 12.094 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.404 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2783 1149 5.1 %RANDOM
Rwork0.2447 ---
obs0.2464 21586 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 200.27 Å2 / Biso mean: 70 Å2 / Biso min: 46.88 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å2-0 Å2-0 Å2
2--1.18 Å2-0 Å2
3----2.35 Å2
Refinement stepCycle: final / Resolution: 2.62→32.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3242 0 0 20 3262
Biso mean---78.12 -
Num. residues----414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133294
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173150
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.6344460
X-RAY DIFFRACTIONr_angle_other_deg1.3391.5837196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9785412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26621.869198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6915556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.051530
X-RAY DIFFRACTIONr_chiral_restr0.0580.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023810
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02798
LS refinement shellResolution: 2.62→2.685 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.329 77 -
Rwork0.315 1441 -
obs--91.01 %

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