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- PDB-1b4p: CRYSTAL STRUCTURES OF CLASS MU CHIMERIC GST ISOENZYMES M1-2 AND M2-1 -

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Basic information

Entry
Database: PDB / ID: 1b4p
TitleCRYSTAL STRUCTURES OF CLASS MU CHIMERIC GST ISOENZYMES M1-2 AND M2-1
ComponentsPROTEIN (GLUTATHIONE S-TRANSFERASE)
KeywordsTRANSFERASE / CHIMERIC GST
Function / homology
Function and homology information


response to catechin / Paracetamol ADME / Azathioprine ADME / Glutathione conjugation / nitrobenzene metabolic process / cellular detoxification of nitrogen compound / response to genistein / hepoxilin biosynthetic process / glutathione binding / linoleic acid metabolic process ...response to catechin / Paracetamol ADME / Azathioprine ADME / Glutathione conjugation / nitrobenzene metabolic process / cellular detoxification of nitrogen compound / response to genistein / hepoxilin biosynthetic process / glutathione binding / linoleic acid metabolic process / glutathione peroxidase activity / response to metal ion / cellular response to caffeine / glutathione transferase / glutathione transferase activity / xenobiotic catabolic process / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / glutathione metabolic process / xenobiotic metabolic process / sarcoplasmic reticulum / fatty acid binding / sensory perception of smell / signaling receptor binding / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Glutathione S-transferase, Mu class / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutathione S-transferase, Mu class / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Soluble glutathione S-transferase N-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
Chem-GPS / Glutathione S-transferase Mu 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsXiao, G. / Chen, J. / Armstrong, R.N. / Gilliland, G.L.
Citation
Journal: To be Published
Title: Crystal Structures of Class MU Chimeric GST Isoenzymes M1-2 and M2-1
Authors: Xiao, G. / Liu, X. / Ji, X. / Zhang, P. / Johnson, W.W. / Chen, J. / Parsons, J.F. / Stevens, W.J. / Gilliland, G.L. / Armstrong, R.N.
#1: Journal: Biochemistry / Year: 1996
Title: First-Sphere and Second-Sphere Electrostatic Effects in the Active Site of a Class Mu Glutathione S-Transferease
Authors: Ji, X. / Zhang, P. / Johnson, W.W. / Sesay, M.A. / Dickert, L. / Prasad, S.S. / Ammon, H.L. / Armstrong, R.N. / Gilliland, G.L.
#2: Journal: Biochemistry / Year: 1994
Title: Structure and Function of the Xenobiotic Substrate Binding Site of a Glutathione S-Transferease as Revealed by X-Ray Crystallogaphic Anaysis of Product Complexes with the Diastereomers of 9-(S- ...Title: Structure and Function of the Xenobiotic Substrate Binding Site of a Glutathione S-Transferease as Revealed by X-Ray Crystallogaphic Anaysis of Product Complexes with the Diastereomers of 9-(S-Glutathionyl)-10-Hydroxy-9,10- Dihydrophenanthren E
Authors: Ji, X. / Zhang, P. / Armstrong, R.N. / Gilliland, G.L.
#3: Journal: Biochemistry / Year: 1992
Title: The Three-Dimensional Structure of a Glutathione S-Transferease from the Mu Gene Class. Structural Analysis of the Binary Complex of Isoenzyme 3-3 and Glutathione at 2.2-A Resolution
History
DepositionDec 26, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 8, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Aug 9, 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 / 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 / _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

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Assembly

Deposited unit
A: PROTEIN (GLUTATHIONE S-TRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0326
Polymers25,7411
Non-polymers1,2915
Water4,504250
1
A: PROTEIN (GLUTATHIONE S-TRANSFERASE)
hetero molecules

A: PROTEIN (GLUTATHIONE S-TRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,06412
Polymers51,4812
Non-polymers2,58310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
Length a, b, c (Å)73.590, 82.550, 79.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

21A-549-

HOH

31A-550-

HOH

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Components

#1: Protein PROTEIN (GLUTATHIONE S-TRANSFERASE) / GST


Mass: 25740.738 Da / Num. of mol.: 1 / Fragment: COMPLETE PROTEIN
Source method: isolated from a genetically manipulated source
Details: SUBSTRATE IS (9S, 10S)-9-(S-GLUTATHIONYL)-10-HYDROXY-9.10-DIHYDROPHENANTHRENE
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: M5219
Description: THE ENZYME IS A CHIMERIC GST, CONSISTING OF DOMAIN I FROM TYPE M1-1 AND DOMAIN II FROM TYPE M2-2
Gene: CDNA INSERT OF CLONE PGT33MX / Organ: LIVER / Plasmid: PGT33MX / Gene (production host): CDNA INSERT OF CLONE PGT33MX / Production host: Escherichia coli (E. coli) / Strain (production host): M5219 / References: UniProt: P08010, glutathione transferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GPS / L-gamma-glutamyl-S-[(9S,10S)-10-hydroxy-9,10-dihydrophenanthren-9-yl]-L-cysteinylglycine


Mass: 501.552 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H27N3O7S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFOR THIS CHIMERIC GST M1-2, THE SEQUENCE IN DOMAIN I IS IDENTICAL TO THAT IN M1-1 AND THE SEQUENCE ...FOR THIS CHIMERIC GST M1-2, THE SEQUENCE IN DOMAIN I IS IDENTICAL TO THAT IN M1-1 AND THE SEQUENCE IN DOMAIN II TO THAT IN M2-2

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growpH: 8
Details: PROTEIN CONC. 10 MG/ML, 25 MM TRIS BUFFER (PH 8.0), 1 MM EDTA, 0.3% OCTYL BETA- D-GLUCOPYRANOSIDE, 2 MM PRODUCT INHIBITOR (GPS)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER / Wavelength: 1.5418
DetectorType: BRUKER / Detector: AREA DETECTOR / Date: Apr 15, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 27013 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rsym value: 0.088 / Net I/σ(I): 8.6
Reflection shellResolution: 1.7→1.81 Å / Redundancy: 36 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.44 / % possible all: 89.7

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
GPRLSArefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GST

1gst
PDB Unreleased entry


Resolution: 1.7→6 Å / σ(F): 2
RfactorNum. reflection% reflection
obs0.179 23933 88.6 %
all-26548 -
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 85 250 2148
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.02
X-RAY DIFFRACTIONp_angle_d0.0420.036
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0480.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0421
X-RAY DIFFRACTIONp_mcangle_it1.6581.5
X-RAY DIFFRACTIONp_scbond_it1.921.5
X-RAY DIFFRACTIONp_scangle_it2.9372
X-RAY DIFFRACTIONp_plane_restr0.0250.03
X-RAY DIFFRACTIONp_chiral_restr0.2650.02
X-RAY DIFFRACTIONp_singtor_nbd0.2040.3
X-RAY DIFFRACTIONp_multtor_nbd0.2070.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2320.3
X-RAY DIFFRACTIONp_planar_tor4.15
X-RAY DIFFRACTIONp_staggered_tor19.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.115
X-RAY DIFFRACTIONp_special_tor

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