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- PDB-1nr7: Crystal structure of apo bovine glutamate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 1nr7
TitleCrystal structure of apo bovine glutamate dehydrogenase
ComponentsGlutamate dehydrogenase 1
KeywordsOXIDOREDUCTASE / apo bovine glutamate dehydrogenase regulation allostery
Function / homology
Function and homology information


glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / glutamine metabolic process / mitochondrial inner membrane / GTP binding / endoplasmic reticulum ...glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / 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
Glutamate dehydrogenase 1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
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 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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

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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
G: Glutamate dehydrogenase 1
H: Glutamate dehydrogenase 1
I: Glutamate dehydrogenase 1
J: Glutamate dehydrogenase 1
K: Glutamate dehydrogenase 1
L: Glutamate dehydrogenase 1


Theoretical massNumber of molelcules
Total (without water)661,33912
Polymers661,33912
Non-polymers00
Water00
1
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)330,6706
Polymers330,6706
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30850 Å2
ΔGint-136 kcal/mol
Surface area107660 Å2
MethodPISA
2
G: Glutamate dehydrogenase 1
H: Glutamate dehydrogenase 1
I: Glutamate dehydrogenase 1
J: Glutamate dehydrogenase 1
K: Glutamate dehydrogenase 1
L: Glutamate dehydrogenase 1


Theoretical massNumber of molelcules
Total (without water)330,6706
Polymers330,6706
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30830 Å2
ΔGint-138 kcal/mol
Surface area107290 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area65430 Å2
ΔGint-291 kcal/mol
Surface area211210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.460, 172.060, 440.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 55111.613 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: liver / Organelle: mitochondria
References: UniProt: P00366, 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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: sodium phosphate, sodium chloride, PEG 8000, MPD, sodium azide, OBG, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
PH range low: 6.8 / PH range high: 6.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 %glycerol suspension1drop
20.1 Msodium phosphate1droppH6.7-6.8
310 mg/mlprotein1drop
410 %(w/v)PEG80001reservoir
50.8 M1reservoirNaCl
64 %(v/v)MPD1reservoir
71 mMsodium azide1reservoir
80.1 Msodium phophate1reservoirpH6.7-6.8
90.75-1.5 %(w/v)octyl-beta-glucopyranoside1reservoir

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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: Jan 1, 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→20 Å / Num. all: 110258 / Num. obs: 102240 / % possible obs: 92 % / Observed criterion σ(I): 1
Reflection shellResolution: 3.2→3.3 Å / % possible all: 90
Reflection
*PLUS
Highest resolution: 3.3 Å / % possible obs: 74.5 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 43.1 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 4.1

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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: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.301 5097 5 %RANDOM
Rwork0.218 ---
all0.24 107071 --
obs0.2181 101143 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.5476 Å2 / ksol: 0.264698 e/Å3
Displacement parametersBiso mean: 53.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2--2.95 Å20 Å2
3----4.04 Å2
Refine analyzeLuzzati coordinate error free: 0.52 Å / Luzzati sigma a free: 0.57 Å
Refinement stepCycle: LAST / Resolution: 3.3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46488 0 0 0 46488
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it14.971.5
X-RAY DIFFRACTIONc_mcangle_it19.562
X-RAY DIFFRACTIONc_scbond_it19.162
X-RAY DIFFRACTIONc_scangle_it23.052.5
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 633 5.2 %
Rwork0.279 11470 -
obs--66.4 %
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: 0.292 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
LS refinement shell
*PLUS
Rfactor Rfree: 0.367 / Rfactor Rwork: 0.273

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