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- PDB-5d3o: Crystal structure of full length human glutaminase C expressed in... -

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Basic information

Entry
Database: PDB / ID: 5d3o
TitleCrystal structure of full length human glutaminase C expressed in E.coli
ComponentsGlutaminase kidney isoform, mitochondrial
KeywordsHYDROLASE / Glutaminase C / GAC
Function / homology
Function and homology information


glutamine catabolic process / regulation of respiratory gaseous exchange by nervous system process / glutamate biosynthetic process / Glutamate and glutamine metabolism / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes ...glutamine catabolic process / regulation of respiratory gaseous exchange by nervous system process / glutamate biosynthetic process / Glutamate and glutamine metabolism / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes / chemical synaptic transmission / protein homotetramerization / mitochondrial matrix / synapse / mitochondrion / 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 / Beta-lactamase/transpeptidase-like / Ankyrin repeat-containing domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutaminase kidney isoform, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.791 Å
AuthorsHuang, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-103485 United States
CitationJournal: To Be Published
Title: Crystal structure of full length human glutaminase C expressed in E.coli
Authors: Huang, Q.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Advisory / Data collection / Derived calculations
Category: diffrn_detector / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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


Theoretical massNumber of molelcules
Total (without water)116,0482
Polymers116,0482
Non-polymers00
Water00
1
A: Glutaminase kidney isoform, mitochondrial
B: Glutaminase kidney isoform, mitochondrial

A: Glutaminase kidney isoform, mitochondrial
B: Glutaminase kidney isoform, mitochondrial


Theoretical massNumber of molelcules
Total (without water)232,0964
Polymers232,0964
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554x,-y,-z-11
Buried area8140 Å2
ΔGint-41 kcal/mol
Surface area60620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.609, 139.371, 179.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Glutaminase kidney isoform, mitochondrial / GLS / K-glutaminase / L-glutamine amidohydrolase


Mass: 58023.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLS, GLS1, KIAA0838 / Plasmid: pSUMO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O94925, glutaminase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 15% PEG6000, 1.0M LiCl, 0.1M Tris-HCL, pH8.0 / PH range: 7.5-8.5 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 32955 / % possible obs: 99.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 16.4

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.791→37.772 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.98 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2657 1455 5 %
Rwork0.2141 --
obs0.2167 29104 87.69 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.267 Å2 / ksol: 0.314 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-41.1713 Å2-0 Å2-0 Å2
2---25.6208 Å2-0 Å2
3----15.5505 Å2
Refinement stepCycle: LAST / Resolution: 2.791→37.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6082 0 0 0 6082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096212
X-RAY DIFFRACTIONf_angle_d1.1578371
X-RAY DIFFRACTIONf_dihedral_angle_d16.5242279
X-RAY DIFFRACTIONf_chiral_restr0.08920
X-RAY DIFFRACTIONf_plane_restr0.0051075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7914-2.89120.4061140.39662083X-RAY DIFFRACTION67
2.8912-3.00690.47431400.35972345X-RAY DIFFRACTION77
3.0069-3.14370.43891510.35252575X-RAY DIFFRACTION84
3.1437-3.30930.38861150.29972717X-RAY DIFFRACTION86
3.3093-3.51650.31661300.25372741X-RAY DIFFRACTION88
3.5165-3.78780.30721540.20052867X-RAY DIFFRACTION92
3.7878-4.16850.20111580.17892861X-RAY DIFFRACTION91
4.1685-4.77070.1771770.15422998X-RAY DIFFRACTION95
4.7707-6.00670.22631640.19283173X-RAY DIFFRACTION99
6.0067-37.77520.25161520.1893289X-RAY DIFFRACTION97

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