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- PDB-8ilj: S-formylglutathione hydrolase (BuSFGH) from Burkholderiaceae sp. -

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Basic information

Entry
Database: PDB / ID: 8ilj
TitleS-formylglutathione hydrolase (BuSFGH) from Burkholderiaceae sp.
ComponentsS-formylglutathione hydrolase
KeywordsHYDROLASE / S-formylglutathione hydrolase
Function / homology
Function and homology information


S-formylglutathione hydrolase / S-formylglutathione hydrolase activity / formaldehyde catabolic process / carboxylic ester hydrolase activity / cytosol
Similarity search - Function
S-formylglutathione hydrolase / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
S-formylglutathione hydrolase
Similarity search - Component
Biological speciesBurkholderiaceae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsHwang, J. / Lee, J.H. / Do, H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)PM22030 Korea, Republic Of
CitationJournal: Crystals / Year: 2023
Title: Crystal structure and functional characterization of an S-formylglutathione hydrolase (BuSFGH) from Burkholderiaceae sp.
Authors: Hwang, J. / Do, H. / Shim, Y.S. / Lee, J.H.
History
DepositionMar 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-formylglutathione hydrolase
B: S-formylglutathione hydrolase


Theoretical massNumber of molelcules
Total (without water)61,6802
Polymers61,6802
Non-polymers00
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Dimer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-7 kcal/mol
Surface area20840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.370, 109.290, 112.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 S-formylglutathione hydrolase


Mass: 30839.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderiaceae (bacteria) / Gene: PAMC26510_23250 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A242MJ43, S-formylglutathione hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium citrate pH 5.0 and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.73→29.52 Å / Num. obs: 65529 / % possible obs: 99.7 % / Redundancy: 12.5 % / Biso Wilson estimate: 19.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08096 / Net I/σ(I): 20.63
Reflection shellResolution: 1.73→1.76 Å / Rmerge(I) obs: 0.3969 / Num. unique obs: 6421 / CC1/2: 0.969

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PHENIX1.15.2refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→29.52 Å / SU ML: 0.1876 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.8011 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2098 3277 5 %
Rwork0.1947 62250 -
obs0.1954 65527 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.77 Å2
Refinement stepCycle: LAST / Resolution: 1.73→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4356 0 0 416 4772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01054480
X-RAY DIFFRACTIONf_angle_d1.14846082
X-RAY DIFFRACTIONf_chiral_restr0.0705640
X-RAY DIFFRACTIONf_plane_restr0.0066798
X-RAY DIFFRACTIONf_dihedral_angle_d20.96351576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.760.2451380.2352613X-RAY DIFFRACTION98.14
1.76-1.780.2321400.21872659X-RAY DIFFRACTION99.43
1.78-1.810.25741410.21072682X-RAY DIFFRACTION99.72
1.81-1.840.26071400.21192670X-RAY DIFFRACTION99.79
1.84-1.880.27841410.20552676X-RAY DIFFRACTION99.79
1.88-1.910.2091410.20022679X-RAY DIFFRACTION99.79
1.91-1.950.2151400.20352658X-RAY DIFFRACTION99.71
1.95-1.990.20781410.1972678X-RAY DIFFRACTION99.79
1.99-2.040.23211420.20712690X-RAY DIFFRACTION99.79
2.04-2.090.23241420.20412711X-RAY DIFFRACTION100
2.09-2.150.22371410.20992669X-RAY DIFFRACTION99.86
2.15-2.210.22681410.20482678X-RAY DIFFRACTION99.86
2.21-2.280.23931430.20862723X-RAY DIFFRACTION99.83
2.28-2.360.22671420.20362690X-RAY DIFFRACTION99.82
2.36-2.460.27221420.20922704X-RAY DIFFRACTION99.82
2.46-2.570.20051410.19932682X-RAY DIFFRACTION99.72
2.57-2.710.23511430.20232711X-RAY DIFFRACTION99.72
2.71-2.880.23511430.21192712X-RAY DIFFRACTION99.58
2.88-3.10.20621430.20622730X-RAY DIFFRACTION99.69
3.1-3.410.18981450.18982745X-RAY DIFFRACTION99.9
3.41-3.90.18281460.17572776X-RAY DIFFRACTION99.93
3.9-4.910.15441460.15042786X-RAY DIFFRACTION99.9
4.91-100.19261550.18272928X-RAY DIFFRACTION99.97

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