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- PDB-5f8b: Crystallographic Structure of PsoE with Co -

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Basic information

Entry
Database: PDB / ID: 5f8b
TitleCrystallographic Structure of PsoE with Co
ComponentsGlutathione S-transferase, putative
KeywordsTRANSFERASE / GST
Function / homology
Function and homology information


Transferases; Transferring alkyl or aryl groups, other than methyl groups / 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 / Chem-PZS / Glutathione S-transferase psoE
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.54 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 9, 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
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_conn_type.id

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Glutathione S-transferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4814
Polymers27,7161
Non-polymers7663
Water21612
1
A: Glutathione S-transferase, putative
hetero molecules

A: Glutathione S-transferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9638
Polymers55,4312
Non-polymers1,5316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area5310 Å2
ΔGint-31 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.331, 123.331, 75.638
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-301-

CO

21A-412-

HOH

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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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#4: Chemical ChemComp-PZS / (5~{S},8~{S},9~{R})-2-[(~{E})-hex-1-enyl]-8-methoxy-3-methyl-9-oxidanyl-8-(phenylcarbonyl)-1-oxa-7-azaspiro[4.4]non-2-ene-4,6-dione


Mass: 399.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25NO6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3 Å3/Da / Density % sol: 58.94 %
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: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. obs: 21207 / % possible obs: 99.8 % / Redundancy: 11.57 % / Net I/σ(I): 21.38

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
PHASERphasing
Cootmodel building
SCALAdata scaling
RefinementResolution: 2.54→43.626 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2467 2106 9.93 %
Rwork0.1912 --
obs0.1969 21200 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.54→43.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1730 0 50 12 1792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151821
X-RAY DIFFRACTIONf_angle_d1.8232473
X-RAY DIFFRACTIONf_dihedral_angle_d17.001681
X-RAY DIFFRACTIONf_chiral_restr0.064272
X-RAY DIFFRACTIONf_plane_restr0.007321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5399-2.5990.35061370.28541271X-RAY DIFFRACTION100
2.599-2.66390.35981450.28631272X-RAY DIFFRACTION100
2.6639-2.7360.30391400.26371259X-RAY DIFFRACTION100
2.736-2.81640.32821490.25081288X-RAY DIFFRACTION100
2.8164-2.90730.29191380.24411279X-RAY DIFFRACTION100
2.9073-3.01120.32691410.25261283X-RAY DIFFRACTION100
3.0112-3.13180.29831390.25531257X-RAY DIFFRACTION100
3.1318-3.27420.3241400.22791281X-RAY DIFFRACTION100
3.2742-3.44680.27511470.21541278X-RAY DIFFRACTION100
3.4468-3.66270.20631370.18571251X-RAY DIFFRACTION100
3.6627-3.94530.24381440.18731281X-RAY DIFFRACTION100
3.9453-4.3420.21961440.16641274X-RAY DIFFRACTION100
4.342-4.96950.20991380.14211281X-RAY DIFFRACTION100
4.9695-6.25810.17371340.15251278X-RAY DIFFRACTION100
6.2581-43.63230.21191330.15071261X-RAY DIFFRACTION97

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