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- PDB-4flm: S-formylglutathione Hydrolase W197I Variant containing Copper -

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Basic information

Entry
Database: PDB / ID: 4flm
TitleS-formylglutathione Hydrolase W197I Variant containing Copper
ComponentsS-formylglutathione hydrolase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / oxidation sensor motif / esterase activity activation / esterase activity inhibition / cysteine sulfinic acid / Cys-60 / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Glutathione conjugation / S-formylglutathione hydrolase / S-formylglutathione hydrolase activity / formaldehyde catabolic process / carboxylic ester hydrolase activity / metal ion binding / cytosol
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
COPPER (II) ION / S-formylglutathione hydrolase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsLegler, P.M. / Millard, C.B.
CitationJournal: Arch.Biochem.Biophys. / Year: 2012
Title: A role for His-160 in peroxide inhibition of S. cerevisiae S-formylglutathione hydrolase: Evidence for an oxidation sensitive motif.
Authors: Legler, P.M. / Leary, D.H. / Hervey, W.J. / Millard, C.B.
History
DepositionJun 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2714
Polymers68,1442
Non-polymers1272
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-31 kcal/mol
Surface area23120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.826, 49.203, 66.845
Angle α, β, γ (deg.)73.92, 80.44, 62.60
Int Tables number1
Space group name H-MP1

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Components

#1: Protein S-formylglutathione hydrolase / FGH


Mass: 34072.180 Da / Num. of mol.: 2 / Mutation: W197I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YJL068C, HRE299, J1102 / Production host: Escherichia coli (E. coli) / References: UniProt: P40363, S-formylglutathione hydrolase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.17 M ammonium acetate, 0.085 M sodium acetate trihydrate, pH 4.6, 25.5% PEG4000, 15% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Oct 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.41→42.52 Å / Num. all: 20479 / Num. obs: 20473 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 7.16 % / Rsym value: 0.115 / Net I/σ(I): 12.42
Reflection shellResolution: 2.41→2.51 Å / Redundancy: 6.43 % / Mean I/σ(I) obs: 3.86 / Rsym value: 0.3967 / % possible all: 100

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
AMoREphasing
REFMAC5.6.0117refinement
SAINTdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PV1

1pv1


Resolution: 2.41→42.52 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / ESU R: 2.118 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25035 1047 5.1 %RANDOM
Rwork0.19152 ---
obs0.19455 19408 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0.09 Å2-0.07 Å2
2--0.1 Å2-0.01 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.41→42.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4638 0 2 133 4773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.024797
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9426499
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4195573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83524.213235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.28715759
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9591514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213724
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.41→2.472 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 70 -
Rwork0.254 1461 -
obs--99.93 %

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