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- PDB-3cry: Gamma-glutamyl cyclotransferase -

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Basic information

Entry
Database: PDB / ID: 3cry
TitleGamma-glutamyl cyclotransferase
ComponentsGamma-glutamyl cyclotransferase
KeywordsTRANSFERASE / enzyme / cyclotransferase / gamma-glutamyl / oxoproline
Function / homology
Function and homology information


gamma-glutamylcyclotransferase / gamma-glutamylcyclotransferase activity / Glutathione synthesis and recycling / release of cytochrome c from mitochondria / protein homodimerization activity / extracellular exosome / cytosol
Similarity search - Function
Gamma-glutamylcyclotransferase / AIG2-like family / Gamma-glutamyl cyclotransferase-like / Hypothetical upf0131 protein ytfp / Gamma-glutamyl cyclotransferase-like / Gamma-glutamyl cyclotransferase-like superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Gamma-glutamylcyclotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOakley, A.J. / Board, P.G.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The identification and structural characterization of C7orf24 as gamma-glutamyl cyclotransferase. An essential enzyme in the gamma-glutamyl cycle
Authors: Oakley, A.J. / Yamada, T. / Liu, D. / Coggan, M. / Clark, A.G. / Board, P.G.
History
DepositionApr 8, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-glutamyl cyclotransferase
B: Gamma-glutamyl cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2355
Polymers42,0572
Non-polymers1773
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-0.3 kcal/mol
Surface area15650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.828, 98.135, 100.499
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-glutamyl cyclotransferase / Uncharacterized protein C7orf24


Mass: 21028.705 Da / Num. of mol.: 2 / Mutation: E98Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGCT / Plasmid: pHUE / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O75223
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.04 Å3/Da / Density % sol: 39.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95361 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 15, 2007 / Details: mirrors
RadiationMonochromator: BEAMLINE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95361 Å / Relative weight: 1
ReflectionResolution: 1.7→70.19 Å / Num. all: 38869 / Num. obs: 38628 / % possible obs: 99.4 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 4.6 % / Biso Wilson estimate: 13.73 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 12.6
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 3.7 / Num. unique all: 5449 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-IceICEdata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RBH

2rbh


Resolution: 1.7→22.37 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.05 / SU ML: 0.07 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -1 / σ(I): -1 / ESU R: 0.114 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22313 1934 5 %RANDOM
Rwork0.17757 ---
obs0.17983 36634 99.23 %-
all-38869 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.957 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2--0.59 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.7→22.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2828 0 12 401 3241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222918
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9653965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3615379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85625.603141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20815553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8011511
X-RAY DIFFRACTIONr_chiral_restr0.0930.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022237
X-RAY DIFFRACTIONr_nbd_refined0.2070.21308
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21984
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2279
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.240
X-RAY DIFFRACTIONr_mcbond_it0.8641.51824
X-RAY DIFFRACTIONr_mcangle_it1.3322863
X-RAY DIFFRACTIONr_scbond_it2.06731267
X-RAY DIFFRACTIONr_scangle_it3.3124.51081
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 146 -
Rwork0.225 2651 -
obs--97.66 %

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