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- PDB-5fhi: Crystallographic structure of PsoE without Co -

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Basic information

Entry
Database: PDB / ID: 5fhi
TitleCrystallographic structure of PsoE without Co
ComponentsGlutathione S-transferase, putative
KeywordsTRANSFERASE / GST
Function / homology
Function and homology information


Transferases; Transferring alkyl or aryl groups, other than methyl groups / glutathione metabolic process / transferase activity / nucleus / cytoplasm
Similarity search - Function
Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal ...Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTATHIONE / Glutathione S-transferase psoE
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.41 Å
AuthorsHara, K. / Hashimoto, H. / Yamamoto, T. / Tsunematsu, Y. / Watanabe, K.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2016
Title: Oxidative trans to cis Isomerization of Olefins in Polyketide Biosynthesis.
Authors: Yamamoto, T. / Tsunematsu, Y. / Hara, K. / Suzuki, T. / Kishimoto, S. / Kawagishi, H. / Noguchi, H. / Hashimoto, H. / Tang, Y. / Hotta, K. / Watanabe, K.
History
DepositionDec 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_volume / _citation.page_first / _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: Glutathione S-transferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0232
Polymers27,7161
Non-polymers3071
Water43224
1
A: Glutathione S-transferase, putative
hetero molecules

A: Glutathione S-transferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0464
Polymers55,4312
Non-polymers6152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area4780 Å2
ΔGint-28 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.413, 145.413, 51.266
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Glutathione S-transferase, putative /


Mass: 27715.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_8G00580 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4WB03
#2: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.42 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEGmme 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.41→50 Å / Num. obs: 12786 / % possible obs: 99.8 % / Redundancy: 19.45 % / Net I/σ(I): 30.54

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
AutoSolphasing
PHASERphasing
Cootmodel building
SCALAdata scaling
RefinementResolution: 2.41→47.598 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.56 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2456 1279 10.05 %
Rwork0.1847 --
obs0.1908 12786 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.41→47.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1730 0 20 24 1774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151789
X-RAY DIFFRACTIONf_angle_d1.4482424
X-RAY DIFFRACTIONf_dihedral_angle_d16.86655
X-RAY DIFFRACTIONf_chiral_restr0.059268
X-RAY DIFFRACTIONf_plane_restr0.01314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4104-2.45960.38751360.31131201X-RAY DIFFRACTION96
2.4596-2.5130.34931360.27331227X-RAY DIFFRACTION100
2.513-2.57150.24491420.22771252X-RAY DIFFRACTION100
2.5715-2.63580.2771400.2461210X-RAY DIFFRACTION100
2.6358-2.70710.28521370.22841276X-RAY DIFFRACTION100
2.7071-2.78670.27871390.23051223X-RAY DIFFRACTION100
2.7867-2.87660.33081390.23271231X-RAY DIFFRACTION100
2.8766-2.97940.31531370.21381242X-RAY DIFFRACTION100
2.9794-3.09870.27371430.22011234X-RAY DIFFRACTION100
3.0987-3.23970.28491410.21151239X-RAY DIFFRACTION100
3.2397-3.41050.29611380.21341244X-RAY DIFFRACTION100
3.4105-3.62410.29821390.19261235X-RAY DIFFRACTION100
3.6241-3.90380.2451370.17591236X-RAY DIFFRACTION100
3.9038-4.29640.23211340.15351252X-RAY DIFFRACTION100
4.2964-4.91750.18371410.13641241X-RAY DIFFRACTION100
4.9175-6.19340.17891340.15871237X-RAY DIFFRACTION100
6.1934-47.60680.19351370.15421255X-RAY DIFFRACTION100

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