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- PDB-6jzl: S-formylglutathione hydrolase homolog from a psychrophilic bacter... -

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Basic information

Entry
Database: PDB / ID: 6jzl
TitleS-formylglutathione hydrolase homolog from a psychrophilic bacterium of Shewanella frigidimarina
ComponentsS-formylglutathione hydrolase
KeywordsHYDROLASE / S-formylglutathione hydrolase / Shewanella frigidimarina
Function / homology
Function and homology information


S-formylglutathione hydrolase / S-formylglutathione hydrolase activity / formaldehyde catabolic process / carboxylic ester hydrolase activity
Similarity search - Function
S-formylglutathione hydrolase / Esterase-like / Putative esterase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-formylglutathione hydrolase
Similarity search - Component
Biological speciesShewanella frigidimarina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsLee, C.W. / Lee, J.H.
CitationJournal: Microb. Cell Fact. / Year: 2019
Title: Structural and functional characterization of a novel cold-active S-formylglutathione hydrolase (SfSFGH) homolog from Shewanella frigidimarina, a psychrophilic bacterium.
Authors: Lee, C.W. / Yoo, W. / Park, S.H. / Le, L.T.H.L. / Jeong, C.S. / Ryu, B.H. / Shin, S.C. / Kim, H.W. / Park, H. / Kim, K.K. / Kim, T.D. / Lee, J.H.
History
DepositionMay 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,1342
Polymers62,1342
Non-polymers00
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-6 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.356, 76.594, 64.725
Angle α, β, γ (deg.)90.00, 105.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein S-formylglutathione hydrolase


Mass: 31066.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella frigidimarina (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q07XK4, S-formylglutathione hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 1.9 Å3/Da / Density % sol: 35.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M lithium chloride and 16% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 19691 / % possible obs: 97 % / Redundancy: 3.5 % / Net I/σ(I): 42.7
Reflection shellResolution: 2.32→2.36 Å / Num. unique obs: 911

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MxDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→33.81 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.723 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 1.121 / ESU R Free: 0.276 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23523 964 4.9 %RANDOM
Rwork0.15753 ---
obs0.16139 18706 96.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.877 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.32→33.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4341 0 0 208 4549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134459
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173947
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.6356054
X-RAY DIFFRACTIONr_angle_other_deg1.3371.5719175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0295552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07723.077234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.34315700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7191520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02958
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1392.6052214
X-RAY DIFFRACTIONr_mcbond_other2.1262.6032212
X-RAY DIFFRACTIONr_mcangle_it3.2663.9022764
X-RAY DIFFRACTIONr_mcangle_other3.2633.9022764
X-RAY DIFFRACTIONr_scbond_it2.6982.8962245
X-RAY DIFFRACTIONr_scbond_other2.6972.8972246
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2614.2083291
X-RAY DIFFRACTIONr_long_range_B_refined5.67430.3565049
X-RAY DIFFRACTIONr_long_range_B_other5.61730.2225019
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.318→2.378 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 47 -
Rwork0.165 1341 -
obs--92.84 %

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