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- PDB-5xtu: Crystal Structure of GDSL Esterase of Photobacterium sp. J15 -

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Basic information

Entry
Database: PDB / ID: 5xtu
TitleCrystal Structure of GDSL Esterase of Photobacterium sp. J15
ComponentsGDSL-family esterase
KeywordsHYDROLASE / GDSL / SGNH / esterase / Photobacterium
Function / homologyGDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily / hydrolase activity, acting on ester bonds / extracellular region / CACODYLATE ION / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / GDSL-family esterase
Function and homology information
Biological speciesPhotobacterium sp. J15 (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.38 Å
AuthorsMazlan, S.N.H.S. / Jonet, M.A. / Leow, T.C. / Ali, M.S.M. / Rahman, R.N.Z.R.A.
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: Crystallization and structure elucidation of GDSL esterase of Photobacterium sp. J15.
Authors: Mazlan, S.N.H.S. / Ali, M.S.M. / Rahman, R.N.Z.R.A. / Sabri, S. / Jonet, M.A. / Leow, T.C.
History
DepositionJun 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Structure summary / Category: audit_author / entity / Item: _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GDSL-family esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8099
Polymers39,1021
Non-polymers7088
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-19 kcal/mol
Surface area13730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.182, 66.461, 105.468
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GDSL-family esterase


Mass: 39101.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium sp. J15(2011) (bacteria)
Strain: 2011 / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosettagami(DE3)pLysS / References: UniProt: A0A0K0PV22

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Non-polymers , 7 types, 444 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.42 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.10 M ammonium sulphate, 0.15 M sodium cacodylate trihydrate pH 6.5, and 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: CCD / Date: Jul 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.38→56.23 Å / Num. obs: 70491 / % possible obs: 98.2 % / Redundancy: 2 % / CC1/2: 0.912 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.07 / Net I/σ(I): 25
Reflection shellResolution: 1.38→1.43 Å / Redundancy: 1.98 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 5.7 / % possible all: 95.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.38→56.23 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.773 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.054
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.179 3478 4.9 %RANDOM
Rwork0.1579 ---
obs0.159 67010 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 66.98 Å2 / Biso mean: 12.254 Å2 / Biso min: 3.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å2-0 Å2
2---0.36 Å20 Å2
3---0.37 Å2
Refinement stepCycle: final / Resolution: 1.38→56.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 33 436 2985
Biso mean--24.02 22.84 -
Num. residues----328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192661
X-RAY DIFFRACTIONr_bond_other_d0.0030.022502
X-RAY DIFFRACTIONr_angle_refined_deg2.5241.9393612
X-RAY DIFFRACTIONr_angle_other_deg1.18335747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2055341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13825.203123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26915430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.929159
X-RAY DIFFRACTIONr_chiral_restr0.1540.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023108
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02635
LS refinement shellResolution: 1.38→1.416 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 257 -
Rwork0.207 4713 -
all-4970 -
obs--94.97 %

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