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- PDB-8hwp: Crystal Structure of Mutant GDSL Esterase of Photobacterium sp. J... -

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Basic information

Entry
Database: PDB / ID: 8hwp
TitleCrystal Structure of Mutant GDSL Esterase of Photobacterium sp. J15 S12A in Complex with Butyrate
ComponentsGDSL-family esterase
KeywordsHYDROLASE / GDSL esterase / butyrate / complex
Function / homologyGDSL lipase/esterase / GDSL-like Lipase/Acylhydrolase / SGNH hydrolase superfamily / hydrolase activity, acting on ester bonds / butanoic acid / GDSL-family esterase
Function and homology information
Biological speciesPhotobacterium sp. J15 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsRahman, N.N.A. / Leow, T.C. / Jonet, M.A.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Crystal Structure of Mutant GDSL Esterase of Photobacterium sp. J15 in Complex with Butyrate
Authors: Rahman, N.N.A. / Leow, T.C. / Jonet, M.A.
History
DepositionJan 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)35,7322
Polymers35,6441
Non-polymers881
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.007, 56.626, 119.678
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
#2: Chemical ChemComp-BUA / butanoic acid


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.96 %
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: 1.54178 Å
DetectorType: RIGAKU / Detector: CCD / Date: Apr 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 117000 / % possible obs: 98.6 % / Redundancy: 3 % / Biso Wilson estimate: 16.78 Å2 / CC1/2: 0.79 / Rmerge(I) obs: 0.037 / Net I/σ(I): 20.3
Reflection shellResolution: 1.73→1.73 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.339 / Num. unique obs: 39377 / CC1/2: 0.79 / % possible all: 89.3

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Processing

Software
NameVersionClassification
REFMACrefinement
PHENIX1.16_3549refinement
iMOSFLMdata reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→50 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2747 2037 5.18 %
Rwork0.2406 37271 -
obs0.2424 117000 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 6 0 2521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092575
X-RAY DIFFRACTIONf_angle_d1.0443489
X-RAY DIFFRACTIONf_dihedral_angle_d3.0251502
X-RAY DIFFRACTIONf_chiral_restr0.059383
X-RAY DIFFRACTIONf_plane_restr0.007458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7301-1.77040.34281360.30272309X-RAY DIFFRACTION93
1.7704-1.81460.37871170.29312391X-RAY DIFFRACTION97
1.8146-1.86370.31871240.2652439X-RAY DIFFRACTION99
1.8637-1.91850.30661400.25572449X-RAY DIFFRACTION99
1.9185-1.98050.311420.26632450X-RAY DIFFRACTION99
1.9805-2.05120.30191420.26572459X-RAY DIFFRACTION99
2.0512-2.13330.31591140.25942500X-RAY DIFFRACTION99
2.1333-2.23040.29941290.2612467X-RAY DIFFRACTION99
2.2304-2.3480.271290.24932495X-RAY DIFFRACTION99
2.348-2.4950.28941300.26322497X-RAY DIFFRACTION99
2.495-2.68760.3011290.27062500X-RAY DIFFRACTION99
2.6876-2.95790.28581550.2652507X-RAY DIFFRACTION100
2.9579-3.38560.31791290.24742556X-RAY DIFFRACTION100
3.3856-4.2640.23231600.20622563X-RAY DIFFRACTION100
4.264-32.94570.20211610.17682689X-RAY DIFFRACTION100

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