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- PDB-9pia: Human glutaminase C mutant S482C -

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Basic information

Entry
Database: PDB / ID: 9pia
TitleHuman glutaminase C mutant S482C
ComponentsIsoform 3 of Glutaminase kidney isoform, mitochondrial
KeywordsHYDROLASE / Glutaminase C / S482C mutant
Function / homology
Function and homology information


L-glutamine catabolic process / regulation of respiratory gaseous exchange by nervous system process / glutamate biosynthetic process / Glutamate and glutamine metabolism / glutaminase / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes ...L-glutamine catabolic process / regulation of respiratory gaseous exchange by nervous system process / glutamate biosynthetic process / Glutamate and glutamine metabolism / glutaminase / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / glutaminase activity / suckling behavior / TP53 Regulates Metabolic Genes / protein homotetramerization / chemical synaptic transmission / mitochondrial matrix / synapse / mitochondrion / 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. / Beta-lactamase/transpeptidase-like / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Glutaminase kidney isoform, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsMilano, S.K. / Ulrich, S.M. / Cerione, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Human glutaminase C mutant S482C
Authors: Milano, S.K. / Ulrich, S.M. / Cerione, R.A.
History
DepositionJul 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 3 of Glutaminase kidney isoform, mitochondrial
B: Isoform 3 of Glutaminase kidney isoform, mitochondrial
C: Isoform 3 of Glutaminase kidney isoform, mitochondrial
D: Isoform 3 of Glutaminase kidney isoform, mitochondrial


Theoretical massNumber of molelcules
Total (without water)262,2284
Polymers262,2284
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-43 kcal/mol
Surface area60950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.851, 138.209, 177.122
Angle α, β, γ (deg.)90.00, 93.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Isoform 3 of Glutaminase kidney isoform, mitochondrial / GLS / K-glutaminase / L-glutamine amidohydrolase


Mass: 65556.977 Da / Num. of mol.: 4 / Mutation: S482C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLS, GLS1, KIAA0838 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O94925, glutaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: LiCl, PEG 6000, Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.8857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8857 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 49294 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.987 / CC star: 0.997 / Rpim(I) all: 0.091 / Rrim(I) all: 0.24 / Χ2: 0.361 / Net I/σ(I): 2.3
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allΧ2Rrim(I) all
3-3.057.11.61424040.5230.8290.650.292
3.05-3.117.11.46624200.60.8660.5910.303
3.11-3.1771.21425290.6760.8980.4950.311
3.17-3.236.90.98824470.790.9390.4040.312
3.23-3.36.80.81524180.8390.9550.3370.323
3.3-3.386.50.73824930.8340.9540.3150.324
3.38-3.466.60.58824260.8940.9720.2470.325
3.46-3.567.10.50224550.9260.9810.2010.339
3.56-3.667.20.39825060.9570.9890.1590.342
3.66-3.787.20.30424060.9740.9930.1210.339
3.78-3.917.10.27125060.9780.9940.1090.347
3.91-4.0770.21924020.9820.9950.0890.352
4.07-4.266.80.19225140.9840.9960.0790.351
4.26-4.486.40.14224450.9890.9970.0610.386
4.48-4.767.10.1324790.9930.9980.0520.387
4.76-5.137.20.12424780.9940.9990.050.376
5.13-5.646.90.13324650.9930.9980.0540.379
5.64-6.466.70.12824860.990.9970.0530.389
6.46-8.137.20.0824630.9970.9990.0320.461
8.13-506.60.04225520.9980.9990.0180.5880.046

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→49.61 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 2011 4.22 %
Rwork0.1875 --
obs0.1884 47635 95.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.99→49.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12396 0 0 96 12492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912664
X-RAY DIFFRACTIONf_angle_d1.08317080
X-RAY DIFFRACTIONf_dihedral_angle_d16.3754664
X-RAY DIFFRACTIONf_chiral_restr0.0511884
X-RAY DIFFRACTIONf_plane_restr0.0082200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.060.34671280.33422743X-RAY DIFFRACTION83
3.06-3.140.31791310.31863220X-RAY DIFFRACTION94
3.14-3.240.30291440.30183161X-RAY DIFFRACTION94
3.24-3.340.27731470.28553215X-RAY DIFFRACTION95
3.34-3.460.27091410.23713214X-RAY DIFFRACTION96
3.46-3.60.28411370.21523292X-RAY DIFFRACTION96
3.6-3.760.20591510.19023260X-RAY DIFFRACTION97
3.76-3.960.2031460.18663362X-RAY DIFFRACTION98
3.96-4.210.16531550.16383321X-RAY DIFFRACTION98
4.21-4.530.1721390.13683312X-RAY DIFFRACTION98
4.53-4.990.14451470.1323364X-RAY DIFFRACTION99
4.99-5.710.1961500.15413372X-RAY DIFFRACTION98
5.71-7.190.19611430.1823359X-RAY DIFFRACTION98
7.19-49.610.18451520.15343429X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 6.8253 Å / Origin y: 34.1413 Å / Origin z: -43.9548 Å
111213212223313233
T0.3658 Å20.0131 Å2-0.0048 Å2-0.4234 Å2-0.0031 Å2--0.4647 Å2
L0.0863 °20.0193 °20.0154 °2-0.4989 °20.1698 °2--1.1018 °2
S-0.0298 Å °-0.0017 Å °-0.0117 Å °-0.0001 Å °0.1015 Å °-0.0266 Å °-0.1094 Å °0.0368 Å °-0.0734 Å °
Refinement TLS groupSelection details: all

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