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- PDB-6dhl: Bovine glutamate dehydrogenase complexed with epicatechin-3-galla... -

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Basic information

Entry
Database: PDB / ID: 6dhl
TitleBovine glutamate dehydrogenase complexed with epicatechin-3-gallate (ECG)
ComponentsGlutamate dehydrogenase 1, mitochondrial
KeywordsOXIDOREDUCTASE / ECG / glutamate / dehydrogenase / 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 (NAD+) activity / glutamate dehydrogenase (NADP+) activity / L-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 (NAD+) activity / glutamate dehydrogenase (NADP+) activity / L-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
Chem-XEG / Glutamate dehydrogenase 1, mitochondrial / Glutamate dehydrogenase 1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.624 Å
AuthorsSmith, T.J.
CitationJournal: J. Biol. Chem. / Year: 2011
Title: Green tea polyphenols control dysregulated glutamate dehydrogenase in transgenic mice by hijacking the ADP activation site.
Authors: Li, C. / Li, M. / Chen, P. / Narayan, S. / Matschinsky, F.M. / Bennett, M.J. / Stanley, C.A. / Smith, T.J.
History
DepositionMay 20, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionJul 25, 2018ID: 3QMU
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
G: Glutamate dehydrogenase 1, mitochondrial
H: Glutamate dehydrogenase 1, mitochondrial
I: Glutamate dehydrogenase 1, mitochondrial
J: Glutamate dehydrogenase 1, mitochondrial
K: Glutamate dehydrogenase 1, mitochondrial
L: Glutamate dehydrogenase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)666,84024
Polymers661,53212
Non-polymers5,30812
Water00
1
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)333,42012
Polymers330,7666
Non-polymers2,6546
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36690 Å2
ΔGint-151 kcal/mol
Surface area108390 Å2
MethodPISA
2
G: Glutamate dehydrogenase 1, mitochondrial
H: Glutamate dehydrogenase 1, mitochondrial
I: Glutamate dehydrogenase 1, mitochondrial
J: Glutamate dehydrogenase 1, mitochondrial
K: Glutamate dehydrogenase 1, mitochondrial
L: Glutamate dehydrogenase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,42012
Polymers330,7666
Non-polymers2,6546
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36360 Å2
ΔGint-143 kcal/mol
Surface area107680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.120, 433.180, 95.170
Angle α, β, γ (deg.)90.00, 118.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glutamate dehydrogenase 1, mitochondrial


Mass: 55127.648 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: A0A140T871, UniProt: P00366*PLUS, glutamate dehydrogenase
#2: Chemical
ChemComp-XEG / (2R,3S)-2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-3,4-dihydro-2H-chromen-3-yl 3,4,5-trihydroxybenzoate


Mass: 442.372 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C22H18O10
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 5 mg/mL GDH in 0.4 mM ECG, 3 mM NADPH, 20 mM glutamate, 2:1 with reservoir solution (0.9 M sodium chloride, 50 mM TEA-HCl, 5 mM reduced glutathione, 8~9% PEG8000, 1 M 1,6-hexanediol), VAPOR ...Details: 5 mg/mL GDH in 0.4 mM ECG, 3 mM NADPH, 20 mM glutamate, 2:1 with reservoir solution (0.9 M sodium chloride, 50 mM TEA-HCl, 5 mM reduced glutathione, 8~9% PEG8000, 1 M 1,6-hexanediol), VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2009
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 72322 / % possible obs: 95.01 % / Redundancy: 3 % / Net I/σ(I): 14.8
Reflection shellResolution: 3.6→3.73 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.624→49.706 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.53
RfactorNum. reflection% reflection
Rfree0.3135 3751 5 %
Rwork0.246 --
obs0.2494 74972 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.624→49.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46488 0 384 0 46872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00747904
X-RAY DIFFRACTIONf_angle_d0.81464716
X-RAY DIFFRACTIONf_dihedral_angle_d7.15728464
X-RAY DIFFRACTIONf_chiral_restr0.0466972
X-RAY DIFFRACTIONf_plane_restr0.0068400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6237-3.66950.4298620.32942430X-RAY DIFFRACTION88
3.6695-3.71780.37611330.32222646X-RAY DIFFRACTION99
3.7178-3.76870.36471580.312586X-RAY DIFFRACTION99
3.7687-3.82250.34331340.29432712X-RAY DIFFRACTION100
3.8225-3.87950.39361430.29982674X-RAY DIFFRACTION99
3.8795-3.94010.3721450.29842604X-RAY DIFFRACTION99
3.9401-4.00470.34441350.29252643X-RAY DIFFRACTION99
4.0047-4.07370.35651560.28322636X-RAY DIFFRACTION99
4.0737-4.14780.33891690.29662681X-RAY DIFFRACTION99
4.1478-4.22750.33231450.27582598X-RAY DIFFRACTION99
4.2275-4.31380.33051520.25662679X-RAY DIFFRACTION99
4.3138-4.40750.32681530.26482601X-RAY DIFFRACTION99
4.4075-4.510.2981220.25132659X-RAY DIFFRACTION99
4.51-4.62270.32931310.24472622X-RAY DIFFRACTION98
4.6227-4.74760.3631380.24042628X-RAY DIFFRACTION98
4.7476-4.88710.29211450.22982628X-RAY DIFFRACTION99
4.8871-5.04470.29531400.24982659X-RAY DIFFRACTION99
5.0447-5.22490.31421510.24692620X-RAY DIFFRACTION99
5.2249-5.43380.37161630.26242626X-RAY DIFFRACTION99
5.4338-5.68080.29051550.25722686X-RAY DIFFRACTION100
5.6808-5.97980.40571150.27452692X-RAY DIFFRACTION100
5.9798-6.35380.32421420.26842685X-RAY DIFFRACTION99
6.3538-6.84320.33331170.24652671X-RAY DIFFRACTION100
6.8432-7.52970.32781450.23242655X-RAY DIFFRACTION99
7.5297-8.61440.25941380.19482665X-RAY DIFFRACTION99
8.6144-10.83470.21271330.16412615X-RAY DIFFRACTION97
10.8347-49.71080.27631310.22162620X-RAY DIFFRACTION96

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