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- PDB-1hwy: BOVINE GLUTAMATE DEHYDROGENASE COMPLEXED WITH NAD AND 2-OXOGLUTARATE -

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Basic information

Entry
Database: PDB / ID: 1hwy
TitleBOVINE GLUTAMATE DEHYDROGENASE COMPLEXED WITH NAD AND 2-OXOGLUTARATE
ComponentsGLUTAMATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / allostery / glutamate dehydrogenase / NAD
Function / homology
Function and homology information


glutamate dehydrogenase [NAD(P)+] activity / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NAD+) activity / glutamate dehydrogenase (NADP+) activity / L-glutamate catabolic process / glutamine metabolic process / mitochondrial inner membrane / GTP binding / endoplasmic reticulum ...glutamate dehydrogenase [NAD(P)+] activity / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NAD+) activity / glutamate dehydrogenase (NADP+) activity / L-glutamate catabolic process / glutamine metabolic process / mitochondrial inner membrane / 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
2-OXOGLUTARIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Glutamate dehydrogenase 1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsSmith, T.J. / Peterson, P.E. / Schmidt, T. / Fang, J. / Stanley, C.A.
Citation
Journal: 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.
#1: Journal: Structure / Year: 1999
Title: The Structure of Bovine Glutamate Dehydrogenase Provides Insights Into the Mechanism of Allostery
Authors: Peterson, P.E. / Smith, T.J.
#2: Journal: J.Struct.Biol. / Year: 1997
Title: Crystallization and Characterization of Bovine Liver Glutamate Dehydrogenase
Authors: Peterson, P.E. / Pierce, J. / Smith, T.J.
History
DepositionJan 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: GLUTAMATE DEHYDROGENASE
B: GLUTAMATE DEHYDROGENASE
C: GLUTAMATE DEHYDROGENASE
D: GLUTAMATE DEHYDROGENASE
E: GLUTAMATE DEHYDROGENASE
F: GLUTAMATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,94648
Polymers333,8296
Non-polymers11,11742
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54620 Å2
ΔGint-341 kcal/mol
Surface area95760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.5, 101, 164.6
Angle α, β, γ (deg.)90, 102.2, 90
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.927816, -0.224638, 0.297816), (0.150901, -0.504108, -0.850355), (0.341154, 0.833914, -0.433821)-5.7433, 80.8995, 35.0899
3given(-0.999983, -0.000582, 0.005756), (0.000509, 0.98223, 0.187679), (-0.005763, 0.187679, -0.982214)-2.0443, -7.2018, 77.0526
4given(-0.927307, -0.165168, -0.33589), (-0.154064, -0.64941, 0.744669), (-0.341125, 0.742285, 0.576755)17.1524, 18.3073, -4.9819
5given(-0.927839, 0.220009, -0.301181), (0.220799, -0.326806, -0.918937), (-0.300602, -0.919127, 0.254646)4.2146, 78.425, 58.2758
6given(0.927153, 0.160107, 0.338753), (-0.219882, -0.499551, 0.837915), (0.303381, -0.85136, -0.427955)-18.9745, 9.8774, 85.3834

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Components

#1: Protein
GLUTAMATE DEHYDROGENASE / GDH


Mass: 55638.211 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Cellular location: INNER MITOCHONDRIAL MATRIX / Organ: LIVER / Organelle: MITOCHONDRIA
References: UniProt: P00366, glutamate dehydrogenase [NAD(P)+]
#2: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: sodium phosphate, NaCl, PEG 8000, sodium azide, methyl pentanediol, octyl-b-glucopyranoside, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5 mMNAD+1drop
220 mMalpha-KG1drop
33.25 mg/mlboGDH1drop
40.1 Msodium phosphate1reservoir
51 %octyl-beta-glucopyranoside1reservoir
65 %methyl pentanediol1reservoir
70.5 Msodium chloride1reservoir
81 mMsodium azide1reservoir
91
101

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å
Reflection shellResolution: 3.2→3.4 Å / Rmerge(I) obs: 0.12 / % possible all: 78
Reflection
*PLUS
% possible obs: 79 % / Rmerge(I) obs: 0.123
Reflection shell
*PLUS
% possible obs: 80 % / Rmerge(I) obs: 0.475

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→8 Å / σ(F): 3 /
RfactorSelection details
Rfree0.29 random
Rwork0.23 -
Refinement stepCycle: LAST / Resolution: 3.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23460 0 708 36 24204
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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