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- PDB-3ss5: Crystal structure of mouse Glutaminase C, L-glutamate-bound form -

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Basic information

Entry
Database: PDB / ID: 3ss5
TitleCrystal structure of mouse Glutaminase C, L-glutamate-bound form
ComponentsGlutaminase C
KeywordsHYDROLASE / Glutaminase / L-Glutamine / Mitochondria / Catalysis product
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
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
GLUTAMIC ACID / Glutaminase kidney isoform, mitochondrial / Glutaminase kidney isoform, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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)213,8968
Polymers213,3084
Non-polymers5894
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-37 kcal/mol
Surface area59660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.380, 139.430, 178.390
Angle α, β, γ (deg.)90.00, 93.77, 90.00
Int Tables number4
Space group name H-MP1211

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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-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.93 Å3/Da / Density % sol: 58.03 %
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: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 25, 2010
RadiationMonochromator: Si(111), Double Flat Crystal Monochromator with Fixed-exit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 2.8→42.88 Å / Num. all: 60426 / Num. obs: 59822 / % possible obs: 99 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 / Redundancy: 2.3 % / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 8752 / Rsym value: 0.431 / % possible all: 98.7

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Processing

Software
NameVersionClassification
MAR345data 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: 2.8→19.985 Å / SU ML: 0.82 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 3013 5.05 %RANDOM
Rwork0.2065 ---
obs0.2082 59611 98.86 %-
all-60298 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.793 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-27.5259 Å2-0 Å2-10.3515 Å2
2---13.6675 Å2-0 Å2
3----13.8585 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12288 0 40 214 12542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312594
X-RAY DIFFRACTIONf_angle_d0.70816981
X-RAY DIFFRACTIONf_dihedral_angle_d13.1414641
X-RAY DIFFRACTIONf_chiral_restr0.0571873
X-RAY DIFFRACTIONf_plane_restr0.0032182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.84360.42011200.34952496X-RAY DIFFRACTION98
2.8436-2.89010.40931390.33232529X-RAY DIFFRACTION99
2.8901-2.93980.36391290.30232603X-RAY DIFFRACTION99
2.9398-2.99310.26881470.28622532X-RAY DIFFRACTION99
2.9931-3.05050.32811300.27252559X-RAY DIFFRACTION99
3.0505-3.11250.31441320.2752577X-RAY DIFFRACTION99
3.1125-3.17990.30751450.24362569X-RAY DIFFRACTION99
3.1799-3.25360.2621330.24332550X-RAY DIFFRACTION99
3.2536-3.33460.28151350.22152601X-RAY DIFFRACTION99
3.3346-3.42430.28751190.21792576X-RAY DIFFRACTION99
3.4243-3.52460.22571530.21132550X-RAY DIFFRACTION99
3.5246-3.63770.20451340.2062594X-RAY DIFFRACTION99
3.6377-3.76690.26671350.18982567X-RAY DIFFRACTION99
3.7669-3.91660.22141390.18492621X-RAY DIFFRACTION99
3.9166-4.09340.20731440.16872551X-RAY DIFFRACTION99
4.0934-4.30720.20031490.16382564X-RAY DIFFRACTION99
4.3072-4.5740.19221190.15762654X-RAY DIFFRACTION99
4.574-4.92230.18191420.15762551X-RAY DIFFRACTION99
4.9223-5.40870.21791520.18552577X-RAY DIFFRACTION99
5.4087-6.17110.2621450.21762600X-RAY DIFFRACTION99
6.1711-7.70030.1961370.20822582X-RAY DIFFRACTION99
7.7003-19.98550.18741350.17452595X-RAY DIFFRACTION97

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