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- PDB-7sbm: Human glutaminase C (Y466W) with L-Gln, open conformation -

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Basic information

Entry
Database: PDB / ID: 7sbm
TitleHuman glutaminase C (Y466W) with L-Gln, open conformation
ComponentsIsoform 3 of Glutaminase kidney isoform, mitochondrial
KeywordsHYDROLASE / Complex / Oligomer / Cancer metabolism / Mitochondrial metabolism
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. / ankyrin repeats / Beta-lactamase/transpeptidase-like / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
GLUTAMINE / Glutaminase kidney isoform, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNguyen, T.-T.T. / Cerione, R.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA201402 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122575 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: High-resolution structures of mitochondrial glutaminase C tetramers indicate conformational changes upon phosphate binding.
Authors: Nguyen, T.T. / Ramachandran, S. / Hill, M.J. / Cerione, R.A.
History
DepositionSep 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,5078
Polymers237,9234
Non-polymers5854
Water1,60389
1
A: Isoform 3 of Glutaminase kidney isoform, mitochondrial
D: Isoform 3 of Glutaminase kidney isoform, mitochondrial
hetero molecules

C: Isoform 3 of Glutaminase kidney isoform, mitochondrial
hetero molecules

B: Isoform 3 of Glutaminase kidney isoform, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,5078
Polymers237,9234
Non-polymers5854
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Buried area8340 Å2
ΔGint-44 kcal/mol
Surface area61650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.842, 139.100, 177.435
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUALAALA(chain 'A' and (resid 139 through 149 or resid 151...AA139 - 14880 - 89
12GLNGLNLEULEU(chain 'A' and (resid 139 through 149 or resid 151...AA151 - 18492 - 125
13VALVALASPASP(chain 'A' and (resid 139 through 149 or resid 151...AA193 - 248134 - 189
14ALAALAPROPRO(chain 'A' and (resid 139 through 149 or resid 151...AA254 - 313195 - 254
15LEULEUGLUGLU(chain 'A' and (resid 139 through 149 or resid 151...AA321 - 545262 - 486
26LEULEUALAALA(chain 'B' and (resid 139 through 149 or resid 151 through 314 or resid 321 through 546))BB139 - 14880 - 89
27GLNGLNLEULEU(chain 'B' and (resid 139 through 149 or resid 151 through 314 or resid 321 through 546))BB151 - 18492 - 125
28VALVALASPASP(chain 'B' and (resid 139 through 149 or resid 151 through 314 or resid 321 through 546))BB193 - 248134 - 189
29ALAALAPROPRO(chain 'B' and (resid 139 through 149 or resid 151 through 314 or resid 321 through 546))BB254 - 313195 - 254
210LEULEUGLUGLU(chain 'B' and (resid 139 through 149 or resid 151 through 314 or resid 321 through 546))BB321 - 545262 - 486
311LEULEUALAALA(chain 'C' and (resid 139 through 149 or resid 151...CC139 - 14880 - 89
312GLNGLNLEULEU(chain 'C' and (resid 139 through 149 or resid 151...CC151 - 18492 - 125
313VALVALASPASP(chain 'C' and (resid 139 through 149 or resid 151...CC193 - 248134 - 189
314ALAALAPROPRO(chain 'C' and (resid 139 through 149 or resid 151...CC254 - 313195 - 254
315LEULEUGLUGLU(chain 'C' and (resid 139 through 149 or resid 151...CC321 - 545262 - 486
416LEULEUALAALA(chain 'D' and (resid 139 through 149 or resid 151...DD139 - 14880 - 89
417GLNGLNLEULEU(chain 'D' and (resid 139 through 149 or resid 151...DD151 - 18492 - 125
418VALVALASPASP(chain 'D' and (resid 139 through 149 or resid 151...DD193 - 248134 - 189
419ALAALAPROPRO(chain 'D' and (resid 139 through 149 or resid 151...DD254 - 313195 - 254
420LEULEUGLUGLU(chain 'D' and (resid 139 through 149 or resid 151...DD321 - 545262 - 486

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Components

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


Mass: 59480.629 Da / Num. of mol.: 4 / Mutation: Y466W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLS, GLS1, KIAA0838 / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / References: UniProt: O94925, glutaminase
#2: Chemical
ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 11.5% PEG 6000, 0.95 M LiCl, and 0.1 M Tris pH 8.5 / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2020 / Details: mirror focusing
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→39.3 Å / Num. obs: 60927 / % possible obs: 99.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 34.51 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rpim(I) all: 0.061 / Net I/σ(I): 4.2
Reflection shellResolution: 2.81→2.85 Å / Redundancy: 6.3 % / Num. unique obs: 5953 / CC1/2: 0.948 / CC star: 0.987 / Rpim(I) all: 0.251 / % possible all: 98.52

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000721.2data reduction
HKL-2000721.2data scaling
PHENIX1.15.2_3472phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5d3o

5d3o


Resolution: 2.8→39.29 Å / SU ML: 0.2444 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.9362
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2428 1993 3.28 %
Rwork0.2004 58708 -
obs0.2018 60701 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.77 Å2
Refinement stepCycle: LAST / Resolution: 2.8→39.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12435 0 40 89 12564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009512741
X-RAY DIFFRACTIONf_angle_d1.301217179
X-RAY DIFFRACTIONf_chiral_restr0.06531892
X-RAY DIFFRACTIONf_plane_restr0.00852208
X-RAY DIFFRACTIONf_dihedral_angle_d9.8457625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.27041380.26414037X-RAY DIFFRACTION97.89
2.87-2.950.27581400.2554168X-RAY DIFFRACTION99.7
2.95-3.030.28061410.24864156X-RAY DIFFRACTION99.88
3.03-3.130.26451420.24724152X-RAY DIFFRACTION99.77
3.13-3.240.30081410.22454160X-RAY DIFFRACTION99.84
3.24-3.370.25551410.21474174X-RAY DIFFRACTION99.72
3.37-3.520.25561420.19314197X-RAY DIFFRACTION99.88
3.52-3.710.25741430.18694184X-RAY DIFFRACTION99.91
3.71-3.940.24331420.18224191X-RAY DIFFRACTION99.82
3.94-4.250.20951440.1714214X-RAY DIFFRACTION99.93
4.25-4.670.22091430.15964218X-RAY DIFFRACTION99.79
4.67-5.350.19611440.17014246X-RAY DIFFRACTION99.57
5.35-6.730.25011460.21784264X-RAY DIFFRACTION99.73
6.73-39.290.22551460.19824347X-RAY DIFFRACTION96.94
Refinement TLS params.Method: refined / Origin x: -31.6126421974 Å / Origin y: 14.9492336684 Å / Origin z: -36.4725105079 Å
111213212223313233
T0.392035123582 Å20.0349188459597 Å2-0.0381844662877 Å2-0.0975830668126 Å20.0125762997778 Å2--0.225365841718 Å2
L0.0188800189093 °20.0657591632463 °2-0.0629786261561 °2-0.297674098467 °20.330844356337 °2--0.184009111697 °2
S-0.0164987383006 Å °0.0306543862742 Å °0.0026857556046 Å °-0.0337687537949 Å °0.0586442237507 Å °-0.0680629973035 Å °0.0391696192608 Å °0.021262764606 Å °-0.0440277965608 Å °
Refinement TLS groupSelection details: all

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