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- PDB-3ss3: Crystal structure of mouse Glutaminase C, ligand-free form -

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Basic information

Entry
Database: PDB / ID: 3ss3
TitleCrystal structure of mouse Glutaminase C, ligand-free form
ComponentsGlutaminase C
KeywordsHYDROLASE / Glutaminase / L-Glutamine / Mitochondria
Function / homology
Function and homology information


Glutamate and glutamine metabolism / Glutamate Neurotransmitter Release Cycle / TP53 Regulates Metabolic Genes / glutamine catabolic process / glutamate biosynthetic process / regulation of respiratory gaseous exchange by nervous system process / intracellular glutamate homeostasis / glutaminase / glutaminase activity / suckling behavior ...Glutamate and glutamine metabolism / Glutamate Neurotransmitter Release Cycle / TP53 Regulates Metabolic Genes / glutamine catabolic process / glutamate biosynthetic process / regulation of respiratory gaseous exchange by nervous system process / intracellular glutamate homeostasis / glutaminase / glutaminase activity / suckling behavior / chemical synaptic transmission / protein homotetramerization / mitochondrial matrix / synapse / mitochondrion / identical protein binding / cytosol
Similarity search - Function
Recoverin; domain 1 - #210 / Glutaminase, EF-hand domain / EF-hand domain / Glutaminase / Glutaminase / Recoverin; domain 1 / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. ...Recoverin; domain 1 - #210 / Glutaminase, EF-hand domain / EF-hand domain / Glutaminase / Glutaminase / Recoverin; domain 1 / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutaminase kidney isoform, mitochondrial / Glutaminase kidney isoform, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsAmbrosio, A.L.B. / Dias, S.M.G. / Cerione, R.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Mitochondrial localization and structure-based phosphate activation mechanism of Glutaminase C with implications for cancer metabolism.
Authors: Cassago, A. / Ferreira, A.P. / Ferreira, I.M. / Fornezari, C. / Gomes, E.R. / Greene, K.S. / Pereira, H.M. / Garratt, R.C. / Dias, S.M. / Ambrosio, A.L.
History
DepositionJul 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Glutaminase C
B: Glutaminase C
C: Glutaminase C
D: Glutaminase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,4508
Polymers213,3084
Non-polymers1424
Water19,9071105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8920 Å2
ΔGint-82 kcal/mol
Surface area61460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.260, 138.810, 179.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a tetramer, as modeled in the asymmetric unit.

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Components

#1: Protein
Glutaminase C


Mass: 53326.961 Da / Num. of mol.: 4 / Fragment: unp residues 134-609
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gls, GLS1, mKIAA0838 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2
References: UniProt: Q69ZX9, UniProt: D3Z7P3*PLUS, glutaminase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1105 / 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: 2.9 Å3/Da / Density % sol: 57.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 17% PEG3350, 0.2M NaCl, 0.1M Bis-TRIS, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 30, 2008
RadiationMonochromator: Si 111 CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.42→20 Å / Num. all: 94559 / Num. obs: 89075 / % possible obs: 94.2 % / Observed criterion σ(F): 1.8 / Observed criterion σ(I): 1.8 / Redundancy: 4.2 % / Rsym value: 0.144 / Net I/σ(I): 5.8
Reflection shellResolution: 2.42→2.55 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 13665 / Rsym value: 0.616 / % possible all: 89.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3czd

3czd


Resolution: 2.42→19.934 Å / SU ML: 0.8 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 4439 4.99 %RANDOM
Rwork0.1954 ---
all0.1981 94885 --
obs0.1981 88926 93.72 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.156 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.8079 Å2-0 Å2-0 Å2
2---2.5034 Å2-0 Å2
3----1.3044 Å2
Refinement stepCycle: LAST / Resolution: 2.42→19.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12144 0 4 1105 13253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612403
X-RAY DIFFRACTIONf_angle_d1.0916716
X-RAY DIFFRACTIONf_dihedral_angle_d14.9764568
X-RAY DIFFRACTIONf_chiral_restr0.0851846
X-RAY DIFFRACTIONf_plane_restr0.0062143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.44750.371320.29622614X-RAY DIFFRACTION88
2.4475-2.47620.35741410.28242635X-RAY DIFFRACTION88
2.4762-2.50630.3331320.26712626X-RAY DIFFRACTION89
2.5063-2.5380.32381400.24452668X-RAY DIFFRACTION89
2.538-2.57130.27191420.23322697X-RAY DIFFRACTION91
2.5713-2.60650.30911390.24482720X-RAY DIFFRACTION90
2.6065-2.64360.31941460.23992672X-RAY DIFFRACTION91
2.6436-2.6830.28811390.24992718X-RAY DIFFRACTION91
2.683-2.72480.30541410.22922753X-RAY DIFFRACTION93
2.7248-2.76940.2751540.22212751X-RAY DIFFRACTION92
2.7694-2.8170.27931620.2112721X-RAY DIFFRACTION92
2.817-2.86810.29791450.21042743X-RAY DIFFRACTION93
2.8681-2.92310.26181370.21792798X-RAY DIFFRACTION92
2.9231-2.98260.28421290.2072775X-RAY DIFFRACTION93
2.9826-3.04720.24111330.20162754X-RAY DIFFRACTION92
3.0472-3.11780.2371460.19732789X-RAY DIFFRACTION93
3.1178-3.19550.26781520.18642813X-RAY DIFFRACTION94
3.1955-3.28150.27561490.1942820X-RAY DIFFRACTION94
3.2815-3.37760.27351520.19672826X-RAY DIFFRACTION95
3.3776-3.48610.25741590.19462886X-RAY DIFFRACTION96
3.4861-3.610.20731470.19372890X-RAY DIFFRACTION97
3.61-3.75360.25251470.18382946X-RAY DIFFRACTION97
3.7536-3.92320.22321360.17072978X-RAY DIFFRACTION98
3.9232-4.12830.19961420.15253005X-RAY DIFFRACTION99
4.1283-4.38440.2131680.1512978X-RAY DIFFRACTION99
4.3844-4.71880.19381760.14572983X-RAY DIFFRACTION99
4.7188-5.18610.20211730.16052971X-RAY DIFFRACTION98
5.1861-5.91920.26551730.19892969X-RAY DIFFRACTION97
5.9192-7.39380.25461590.21522916X-RAY DIFFRACTION94
7.3938-19.93490.20811480.18813072X-RAY DIFFRACTION95

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