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- PDB-6dhm: Bovine glutamate dehydrogenase complexed with zinc -

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Basic information

Entry
Database: PDB / ID: 6dhm
TitleBovine glutamate dehydrogenase complexed with zinc
ComponentsGlutamate dehydrogenase 1, mitochondrial
KeywordsOXIDOREDUCTASE / glutamate / dehydrogenase / zinc / inhibition
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 / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSmith, T.J.
CitationJournal: FEBS J. / Year: 2011
Title: A novel mechanism of V-type zinc inhibition of glutamate dehydrogenase results from disruption of subunit interactions necessary for efficient catalysis.
Authors: Bailey, J. / Powell, L. / Sinanan, L. / Neal, J. / Li, M. / Smith, T. / Bell, E.
History
DepositionMay 20, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionJul 25, 2018ID: 3MVQ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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)392,22736
Polymers382,9486
Non-polymers9,27930
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, The active assembly is a hexamer from many experiments
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41250 Å2
ΔGint-639 kcal/mol
Surface area98330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.110, 98.760, 165.640
Angle α, β, γ (deg.)90.00, 101.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glutamate dehydrogenase 1, mitochondrial


Mass: 63824.699 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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn

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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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 8% PEG8000, 0.15 M sodium chloride, 5% MPD, 0.1 M triethanolamine-HCl, pH 7.0, 50 mM monosodium glutamate, 2 mM GTP, 2 mM NADPH, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Sep 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 75820 / % possible obs: 92.92 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Net I/σ(I): 6.1
Reflection shellResolution: 3→3.14 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→45.876 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 27.94
RfactorNum. reflection% reflection
Rfree0.2696 3817 5.03 %
Rwork0.1973 --
obs0.201 75814 92.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→45.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23286 0 552 0 23838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01124382
X-RAY DIFFRACTIONf_angle_d1.16532958
X-RAY DIFFRACTIONf_dihedral_angle_d7.26114458
X-RAY DIFFRACTIONf_chiral_restr0.0593542
X-RAY DIFFRACTIONf_plane_restr0.0074244
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9416-2.97880.3215370.2556907X-RAY DIFFRACTION32
2.9788-3.0180.37471170.25142119X-RAY DIFFRACTION74
3.018-3.05930.35351280.25272610X-RAY DIFFRACTION91
3.0593-3.1030.33941660.24282580X-RAY DIFFRACTION91
3.103-3.14930.33091290.23792670X-RAY DIFFRACTION93
3.1493-3.19850.34091450.23612638X-RAY DIFFRACTION92
3.1985-3.2510.31171440.23252663X-RAY DIFFRACTION94
3.251-3.3070.33371370.23432693X-RAY DIFFRACTION94
3.307-3.36710.32511510.22482618X-RAY DIFFRACTION93
3.3671-3.43190.25441450.21212686X-RAY DIFFRACTION94
3.4319-3.50190.30131250.20482710X-RAY DIFFRACTION94
3.5019-3.5780.27271460.19922739X-RAY DIFFRACTION96
3.578-3.66120.26831600.19332742X-RAY DIFFRACTION96
3.6612-3.75270.27891380.19152742X-RAY DIFFRACTION96
3.7527-3.85420.24231340.19462766X-RAY DIFFRACTION96
3.8542-3.96750.25921320.1812765X-RAY DIFFRACTION96
3.9675-4.09550.25121460.18242799X-RAY DIFFRACTION97
4.0955-4.24180.23011490.17822790X-RAY DIFFRACTION98
4.2418-4.41150.25261500.1762827X-RAY DIFFRACTION99
4.4115-4.61210.24431470.17382848X-RAY DIFFRACTION99
4.6121-4.8550.27041440.16962865X-RAY DIFFRACTION99
4.855-5.15880.23611750.17822830X-RAY DIFFRACTION99
5.1588-5.55650.28371470.1882866X-RAY DIFFRACTION100
5.5565-6.11450.25861740.19172862X-RAY DIFFRACTION100
6.1145-6.99660.24831350.19322901X-RAY DIFFRACTION100
6.9966-8.80470.19271560.17412919X-RAY DIFFRACTION100
8.8047-45.8820.24691600.19622842X-RAY DIFFRACTION95

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