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- PDB-1nr1: Crystal structure of the R463A mutant of human Glutamate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 1nr1
TitleCrystal structure of the R463A mutant of human Glutamate dehydrogenase
ComponentsGlutamate dehydrogenase 1
KeywordsOXIDOREDUCTASE / glutamate dehydrogenase / hexamer / regulation
Function / homology
Function and homology information


L-leucine binding / glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate biosynthetic process / glutamate dehydrogenase (NADP+) activity / Glutamate and glutamine metabolism / glutamate dehydrogenase (NAD+) activity / glutamine metabolic process ...L-leucine binding / glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate biosynthetic process / glutamate dehydrogenase (NADP+) activity / Glutamate and glutamine metabolism / glutamate dehydrogenase (NAD+) activity / glutamine metabolic process / NAD+ binding / Mitochondrial protein degradation / substantia nigra development / ADP binding / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / 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: 3.3 Å
AuthorsBanerjee, S. / Schmidt, T. / Fang, J. / Stanley, C.A. / Smith, T.J.
CitationJournal: Biochemistry / Year: 2003
Title: Structural studies on ADP activation of mammalian glutamate dehydrogenase and the evolution of regulation
Authors: Banerjee, S. / Schmidt, T. / Fang, J. / Stanley, C.A. / Smith, T.J.
History
DepositionJan 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 8, 2017Group: Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)330,1536
Polymers330,1536
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31560 Å2
ΔGint-140 kcal/mol
Surface area106250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.920, 98.640, 124.260
Angle α, β, γ (deg.)86.48, 69.69, 60.87
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: Protein
Glutamate dehydrogenase 1 / E.C.1.4.1.3


Mass: 55025.496 Da / Num. of mol.: 6 / Mutation: R463A
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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: sodium phosphate, PEG 8000, BOG, sodium chloride, MPD, sodium azide, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 Msodium phosphate1droppH6.8
226 mg/mlprotein1drop
310 %(w/v)PEG80001reservoir
40.1 M1reservoirNaCl
51.3 %(w/v)octyl-beta-glucopyranoside1reservoir
67.5 %(v/v)MPD1reservoir
70.1 Msodium phosphate1reservoirpH6.8
81 mMsodium azide1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 6, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 55963 / Num. obs: 50903 / % possible obs: 91 % / Observed criterion σ(I): 1
Reflection shellResolution: 3.3→3.45 Å / % possible all: 63
Reflection
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 20 Å / % possible obs: 64.6 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.032
Reflection shell
*PLUS
% possible obs: 62.9 % / Redundancy: 1.3 % / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→19.99 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 5072 4 %RANDOM
Rwork0.222 ---
all0.24 55963 --
obs0.222 50903 90.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.6123 Å2 / ksol: 0.260803 e/Å3
Displacement parametersBiso mean: 46.6 Å2
Baniso -1Baniso -2Baniso -3
1-10.63 Å22.27 Å2-16.05 Å2
2---6.27 Å2-1.5 Å2
3----4.37 Å2
Refine analyzeLuzzati coordinate error free: 0.51 Å / Luzzati sigma a free: 0.53 Å
Refinement stepCycle: LAST / Resolution: 3.3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23208 0 0 0 23208
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_mcbond_it5.181.5
X-RAY DIFFRACTIONc_mcangle_it7.832
X-RAY DIFFRACTIONc_scbond_it7.552
X-RAY DIFFRACTIONc_scangle_it10.012.5
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 314 4 %
Rwork0.265 7555 -
obs--84.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ADP.PARAMADP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.276 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.98
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24
LS refinement shell
*PLUS
Rfactor Rfree: 0.336 / Rfactor Rwork: 0.283

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