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- PDB-1l1f: Structure of human glutamate dehydrogenase-apo form -

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Basic information

Entry
Database: PDB / ID: 1l1f
TitleStructure of human glutamate dehydrogenase-apo form
ComponentsGlutamate Dehydrogenase 1
KeywordsOXIDOREDUCTASE / Allostery / negative cooperativity
Function / homology
Function and homology information


glutamate dehydrogenase [NAD(P)+] activity / L-leucine binding / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate biosynthetic process / glutamate dehydrogenase (NAD+) activity / glutamate dehydrogenase (NADP+) activity / Glutamate and glutamine metabolism / L-glutamate catabolic process / glutamine metabolic process ...glutamate dehydrogenase [NAD(P)+] activity / L-leucine binding / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate biosynthetic process / glutamate dehydrogenase (NAD+) activity / glutamate dehydrogenase (NADP+) activity / Glutamate and glutamine metabolism / L-glutamate catabolic process / glutamine metabolic process / NAD+ binding / Mitochondrial protein degradation / substantia nigra development / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / ADP binding / mitochondrial matrix / GTP binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / ATP binding / cytoplasm
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
Glutamate dehydrogenase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSmith, T.J. / Schmidt, T. / Fang, J. / Wu, J. / Siuzdak, G. / Stanley, C.A.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The structure of apo human glutamate dehydrogenase details subunit communication and allostery.
Authors: Smith, T.J. / Schmidt, T. / Fang, J. / Wu, J. / Siuzdak, G. / Stanley, C.A.
History
DepositionFeb 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 400COMPOUND NAD binding domain orientation differs among the six chains.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate Dehydrogenase 1
B: Glutamate Dehydrogenase 1
C: Glutamate Dehydrogenase 1
D: Glutamate Dehydrogenase 1
E: Glutamate Dehydrogenase 1
F: Glutamate Dehydrogenase 1


Theoretical massNumber of molelcules
Total (without water)336,5136
Polymers336,5136
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30360 Å2
ΔGint-146 kcal/mol
Surface area103940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.8, 98.8, 124.2
Angle α, β, γ (deg.)86.26, 70.28, 60.34
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Glutamate Dehydrogenase 1 / GDH


Mass: 56085.566 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
References: UniProt: P00367, glutamate dehydrogenase [NAD(P)+]

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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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 8000, NaCl, sodium phosphate, sodium azide, octyl-b-glucopyranoside, methyl pentanediol, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11 %(w/v)octyl-beta-glucopyranoside1reservoir
21 mMsodium azide1reservoir
350 mM1reservoirNaCl
48 %(v/v)methyl pentanediol1reservoir
50.1 Msodium phosphate1reservoirpH7.3
618 mg/mlenzyme1drop
70.1 Msodium phosphate1droppH7.0

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 14, 2001
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 94574 / Num. obs: 91356 / % possible obs: 90.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Rsym value: 0.047
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 94574 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.82 Å / % possible obs: 54.8 % / Num. unique obs: 7168 / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
X-PLORmodel building
Omodel building
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.302 30 5%, X-Plor
Rwork0.262 --
all-86409 -
obs-78217 -
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23244 0 0 0 23244
Software
*PLUS
Name: 0 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 8 Å / σ(F): 2 / Num. reflection Rfree: 30 / % reflection Rfree: 5 % / Rfactor obs: 0.262
Solvent computation
*PLUS
Displacement parameters
*PLUS

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