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- PDB-6dhq: Bovine glutamate dehydrogenase complexed with NADPH, glutamate, a... -

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Basic information

Entry
Database: PDB / ID: 6dhq
TitleBovine glutamate dehydrogenase complexed with NADPH, glutamate, and GTP
ComponentsGlutamate dehydrogenase 1, mitochondrial
KeywordsOXIDOREDUCTASE / glutamate / dehydrogenase / GTP / NADPH / bovine
Function / homology
Function and homology information


Glutamate and glutamine metabolism / Transcriptional activation of mitochondrial biogenesis / glutamate dehydrogenase [NAD(P)+] activity / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / glutamate catabolic process / glutamine metabolic process / Mitochondrial protein degradation ...Glutamate and glutamine metabolism / Transcriptional activation of mitochondrial biogenesis / glutamate dehydrogenase [NAD(P)+] activity / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / glutamate catabolic process / glutamine metabolic process / Mitochondrial protein degradation / positive regulation of insulin secretion / mitochondrial inner membrane / mitochondrial matrix / nucleotide binding / GTP binding / endoplasmic reticulum / mitochondrion / ATP binding / identical protein binding
Similarity search - Function
Helix Hairpins - #140 / Leucine Dehydrogenase, chain A, domain 1 / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal ...Helix Hairpins - #140 / Leucine Dehydrogenase, chain A, domain 1 / NAD(P) binding domain of glutamate dehydrogenase / Leu/Phe/Val dehydrogenases active site / Glu / Leu / Phe / Val dehydrogenases active site. / Glutamate/phenylalanine/leucine/valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, dimerisation domain / Glu/Leu/Phe/Val dehydrogenase, dimerisation domain / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Glutamate/phenylalanine/leucine/valine dehydrogenase, C-terminal / Glutamate/Leucine/Phenylalanine/Valine dehydrogenase / Aminoacid dehydrogenase-like, N-terminal domain superfamily / Helix Hairpins / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / GUANOSINE-5'-TRIPHOSPHATE / Chem-NDP / Glutamate dehydrogenase 1, mitochondrial / Glutamate dehydrogenase 1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSmith, T.J.
CitationJournal: J. Mol. Biol. / Year: 2001
Title: Structures of bovine glutamate dehydrogenase complexes elucidate the mechanism of purine regulation.
Authors: Smith, T.J. / Peterson, P.E. / Schmidt, T. / Fang, J. / Stanley, C.A.
History
DepositionMay 20, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionJul 25, 2018ID: 1HWZ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate dehydrogenase 1, mitochondrial
B: Glutamate dehydrogenase 1, mitochondrial
C: Glutamate dehydrogenase 1, mitochondrial
D: Glutamate dehydrogenase 1, mitochondrial
E: Glutamate dehydrogenase 1, mitochondrial
F: Glutamate dehydrogenase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,78624
Polymers334,2916
Non-polymers8,49418
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, It is well known that the active form of GDH is a hexamer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43290 Å2
ΔGint-165 kcal/mol
Surface area103080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.246, 101.747, 167.852
Angle α, β, γ (deg.)90.00, 102.22, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain A and (resid 4 through 18 or resid 20...
211(chain B and (resid 4 through 18 or resid 20...
311(chain C and (resid 4 through 18 or resid 20...
411(chain D and (resid 4 through 18 or resid 20...
511(chain E and (resid 4 through 18 or resid 20...
611(chain F and (resid 4 through 18 or resid 20...

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Components

#1: Protein
Glutamate dehydrogenase 1, mitochondrial


Mass: 55715.207 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
References: UniProt: A0A140T871, UniProt: P00366*PLUS, glutamate dehydrogenase
#2: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: octyl-b-glucopyranoside, sodium chloride, sodium phosphate, sodium azide, MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2000
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 108403 / % possible obs: 60.24 % / Redundancy: 2.1 % / Net I/σ(I): 17
Reflection shellResolution: 2.3→2.382 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.552 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 32.95
RfactorNum. reflection% reflection
Rfree0.2618 1998 1.84 %
Rwork0.2237 --
obs0.2244 108403 60.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24036 0 0 383 24419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01824564
X-RAY DIFFRACTIONf_angle_d1.81933258
X-RAY DIFFRACTIONf_dihedral_angle_d13.29114568
X-RAY DIFFRACTIONf_chiral_restr0.0943582
X-RAY DIFFRACTIONf_plane_restr0.014284
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3515X-RAY DIFFRACTIONPOSITIONAL
12B3515X-RAY DIFFRACTIONPOSITIONAL0.242
13C3515X-RAY DIFFRACTIONPOSITIONAL0.241
14D3515X-RAY DIFFRACTIONPOSITIONAL0.226
15E3515X-RAY DIFFRACTIONPOSITIONAL0.258
16F3515X-RAY DIFFRACTIONPOSITIONAL0.23
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.35760.3389500.25122626X-RAY DIFFRACTION21
2.3576-2.42130.3076650.27293520X-RAY DIFFRACTION28
2.4213-2.49250.3095870.27314668X-RAY DIFFRACTION37
2.4925-2.57290.29811230.29056534X-RAY DIFFRACTION52
2.5729-2.66480.33451600.27578509X-RAY DIFFRACTION68
2.6648-2.77140.33231760.27659402X-RAY DIFFRACTION75
2.7714-2.89750.32471840.2639776X-RAY DIFFRACTION77
2.8975-3.05010.31821830.2549734X-RAY DIFFRACTION78
3.0501-3.2410.27891820.25469721X-RAY DIFFRACTION77
3.241-3.49080.2861800.24129518X-RAY DIFFRACTION75
3.4908-3.84150.241690.20879085X-RAY DIFFRACTION72
3.8415-4.39580.24421560.19438265X-RAY DIFFRACTION65
4.3958-5.53220.21811470.1877836X-RAY DIFFRACTION62
5.5322-29.55460.21131360.19817211X-RAY DIFFRACTION56

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