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- PDB-2v36: Crystal structure of gamma-glutamyl transferase from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 2v36
TitleCrystal structure of gamma-glutamyl transferase from Bacillus subtilis
Components
  • GAMMA-GLUTAMYLTRANSPEPTIDASE LARGE CHAIN
  • GAMMA-GLUTAMYLTRANSPEPTIDASE SMALL CHAIN
KeywordsTRANSFERASE / GLUTATHIONE BIOSYNTHESIS / GAMMA-GLUTAMYL TRANSFERASE / GAMMA-GLUTAMYL TRANSPEPTIDASE / ACYLTRANSFERASE / ZYMOGEN
Function / homology
Function and homology information


gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / glutathione biosynthetic process / proteolysis / extracellular region
Similarity search - Function
Gamma-glutamyltranspeptidase, small (S) subunit / : / Gamma-glutamyltranspeptidase, large (L) subunit, C-terminal domain / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Serum Albumin; Chain A, Domain 1 / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 ...Gamma-glutamyltranspeptidase, small (S) subunit / : / Gamma-glutamyltranspeptidase, large (L) subunit, C-terminal domain / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Serum Albumin; Chain A, Domain 1 / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutathione hydrolase proenzyme
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSharath, B. / Prabhune, A.A. / Suresh, C.G. / Wilkinson, A.J. / Brannigan, J.A.
CitationJournal: To be Published
Title: Crystal Structure of Gamma-Glutamyl Transferase
Authors: Sharath, B. / Prabhune, A.A. / Suresh, C.G. / Wilkinson, A.J. / Brannigan, J.A.
History
DepositionJun 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GAMMA-GLUTAMYLTRANSPEPTIDASE LARGE CHAIN
B: GAMMA-GLUTAMYLTRANSPEPTIDASE SMALL CHAIN
C: GAMMA-GLUTAMYLTRANSPEPTIDASE LARGE CHAIN
D: GAMMA-GLUTAMYLTRANSPEPTIDASE SMALL CHAIN


Theoretical massNumber of molelcules
Total (without water)125,1074
Polymers125,1074
Non-polymers00
Water6,287349
1
A: GAMMA-GLUTAMYLTRANSPEPTIDASE LARGE CHAIN
B: GAMMA-GLUTAMYLTRANSPEPTIDASE SMALL CHAIN


Theoretical massNumber of molelcules
Total (without water)62,5542
Polymers62,5542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14740 Å2
ΔGint-120.5 kcal/mol
Surface area23420 Å2
MethodPQS
2
C: GAMMA-GLUTAMYLTRANSPEPTIDASE LARGE CHAIN
D: GAMMA-GLUTAMYLTRANSPEPTIDASE SMALL CHAIN


Theoretical massNumber of molelcules
Total (without water)62,5542
Polymers62,5542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14910 Å2
ΔGint-124.2 kcal/mol
Surface area22850 Å2
MethodPQS
Unit cell
Length a, b, c (Å)72.256, 108.766, 161.347
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GAMMA-GLUTAMYLTRANSPEPTIDASE LARGE CHAIN


Mass: 41452.953 Da / Num. of mol.: 2 / Fragment: RESIDUES 29-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PET26B / Production host: Escherichia coli BL21(DE3) / References: UniProt: P54422, gamma-glutamyltransferase
#2: Protein GAMMA-GLUTAMYLTRANSPEPTIDASE SMALL CHAIN


Mass: 21100.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PET26B / Production host: Escherichia coli BL21(DE3) / References: UniProt: P54422, gamma-glutamyltransferase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.7 Å3/Da / Density % sol: 54.2 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1M SODIUM HEPES PH 7.5, 25% PEG 2000K MME AND 0.2M KSCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→29.6 Å / Num. obs: 1952022 / % possible obs: 97.8 % / Observed criterion σ(I): 4.5 / Redundancy: 4.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.8
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.9 / % possible all: 82.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DBU

2dbu


Resolution: 1.85→90.17 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.905 / SU B: 2.916 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS NOT MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.249 5358 5 %RANDOM
Rwork0.22 ---
obs0.221 101881 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å20 Å2
2--1.08 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.85→90.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8023 0 0 349 8372
LS refinement shellResolution: 1.84→1.89 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 288
Rwork0.307 6068

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