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- PDB-8hwo: Crystal Structure of mutant GDSL Esterase of Photobacterium sp. J15 -

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Basic information

Entry
Database: PDB / ID: 8hwo
TitleCrystal Structure of mutant GDSL Esterase of Photobacterium sp. J15
ComponentsGDSL-family esterase
KeywordsHYDROLASE / GDSL esterase
Function / homologyGDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily / hydrolase activity, acting on ester bonds / GDSL-family esterase
Function and homology information
Biological speciesPhotobacterium sp. J15 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsRahman, N.N.A. / Leow, T.C. / Jonet, M.A.
Funding support1items
OrganizationGrant numberCountry
Other government
Citation
Journal: 3 Biotech / Year: 2023
Title: X-ray crystallography of mutant GDSL esterase S12A of Photobacterium marinum J15.
Authors: Rahman, N.N.A. / Sharif, F.M. / Kamarudin, N.H.A. / Ali, M.S.M. / Aris, S.N.A.M. / Jonet, M.A. / Rahman, R.N.Z.R.A. / Sabri, S. / Leow, T.C.
#1: Journal: 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, N.N.A. / Sabri, S. / Jonet, M.A. / Leow, T.C.
History
DepositionJan 1, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GDSL-family esterase


Theoretical massNumber of molelcules
Total (without water)35,6441
Polymers35,6441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.120, 55.820, 120.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein GDSL-family esterase


Mass: 35643.965 Da / Num. of mol.: 1 / Mutation: S12A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium sp. J15 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K0PV22

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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: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate as salt, 30% (w/v) polyethylene glycol 4,000 as precipitant in 0.1 M sodium acetate trihydrate buffer at pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: CCD / Date: Oct 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.96→40 Å / Num. obs: 25427 / % possible obs: 98.6 % / Redundancy: 1.8 % / CC1/2: 1 / Net I/σ(I): 13.4
Reflection shellResolution: 1.96→1.96 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 25427 / CC1/2: 1 / % possible all: 98.38

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
iMOSFLMdata reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XTU

5xtu


Resolution: 1.96→40 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2994 --
Rwork0.2437 --
obs-25427 98.38 %
Refinement stepCycle: LAST / Resolution: 1.96→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 0 0 2515

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