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- PDB-5w2j: Crystal structure of dimeric form of mouse Glutaminase C -

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Basic information

Entry
Database: PDB / ID: 5w2j
TitleCrystal structure of dimeric form of mouse Glutaminase C
Components
  • Glutaminase kidney isoform, mitochondrial
  • unidentified peptide
KeywordsHYDROLASE / Glutamine metabolism / Glutaminase
Function / homology
Function and homology information


Glutamate and glutamine metabolism / Glutamate Neurotransmitter Release Cycle / TP53 Regulates Metabolic Genes / glutamine catabolic process / regulation of respiratory gaseous exchange by nervous system process / glutamate biosynthetic process / intracellular glutamate homeostasis / glutaminase / glutaminase activity / suckling behavior ...Glutamate and glutamine metabolism / Glutamate Neurotransmitter Release Cycle / TP53 Regulates Metabolic Genes / glutamine catabolic process / regulation of respiratory gaseous exchange by nervous system process / glutamate biosynthetic process / intracellular glutamate homeostasis / glutaminase / glutaminase activity / suckling behavior / chemical synaptic transmission / protein homotetramerization / mitochondrial matrix / synapse / identical protein binding / cytosol
Similarity search - Function
Glutaminase, EF-hand domain / EF-hand domain / Glutaminase / Glutaminase / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Glutaminase kidney isoform, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsCerione, R.A. / Li, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P41 RR United States
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Mechanistic Basis of Glutaminase Activation: A KEY ENZYME THAT PROMOTES GLUTAMINE METABOLISM IN CANCER CELLS.
Authors: Li, Y. / Erickson, J.W. / Stalnecker, C.A. / Katt, W.P. / Huang, Q. / Cerione, R.A. / Ramachandran, S.
History
DepositionJun 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Refinement description / Category: refine
Item: _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaminase kidney isoform, mitochondrial
B: Glutaminase kidney isoform, mitochondrial
F: unidentified peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0455
Polymers92,9743
Non-polymers712
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-43 kcal/mol
Surface area32450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.940, 100.880, 145.450
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 Glutaminase kidney isoform, mitochondrial / GLS


Mass: 45836.812 Da / Num. of mol.: 2 / Fragment: UNP residues 141-551 / Mutation: D391K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gls, Gls1, Kiaa0838 / Production host: Escherichia coli (E. coli) / References: UniProt: D3Z7P3, glutaminase
#2: Protein/peptide unidentified peptide


Mass: 1300.481 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 293.15 K / Method: evaporation / pH: 8.5 / Details: 9% PEG8000, 10% glycerol, 50 mM Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 12, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→82.89 Å / Num. obs: 51086 / % possible obs: 92.87 % / Redundancy: 7.3 % / Net I/σ(I): 50.9
Reflection shellHighest resolution: 2.3 Å

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.5→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.22761 --
Rwork0.19641 --
obs-51086 92 %
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6489 0 2 169 6660

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