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- PDB-1nqt: Crystal structure of bovine Glutamate dehydrogenase-ADP complex -

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Basic information

Entry
Database: PDB / ID: 1nqt
TitleCrystal structure of bovine Glutamate dehydrogenase-ADP complex
ComponentsGlutamate dehydrogenase 1
KeywordsOXIDOREDUCTASE / glutamate dehydrogenase-ADP complex / dimer of two hexamers / regulation
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
ADENOSINE-5'-DIPHOSPHATE / Glutamate dehydrogenase 1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.5 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)666,46624
Polymers661,33912
Non-polymers5,12612
Water0
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,23312
Polymers330,6706
Non-polymers2,5636
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36010 Å2
ΔGint-155 kcal/mol
Surface area106710 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,23312
Polymers330,6706
Non-polymers2,5636
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36050 Å2
ΔGint-160 kcal/mol
Surface area106770 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area75800 Å2
ΔGint-331 kcal/mol
Surface area209740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.460, 171.930, 439.680
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: mitochondriaMitochondrion
References: UniProt: P00366, glutamate dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 55.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: sodium phosphate, PEG 8000 sodium azide, sodium chloride, MPD and OBG, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / PH range low: 6.8 / PH range high: 6.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 %glycerol suspension1drop
20.1 Msodium phosphate1droppH6.7-6.8
310 mg/mlprotein1drop
40.1 Msodium phosphate1reservoir
51 %(w/v)octyl-beta-glucopyranoside1reservoir
66 %(v/v)MPD1reservoir
71 Msodium phosphate1reservoir
814 %(w/v)PEG80001reservoir
91 mMsodium azide1reservoir
100.3 mMADP1reservoir

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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: 3.5→30 Å / Num. all: 91015 / Num. obs: 87616 / % possible obs: 96 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.7
Reflection shellResolution: 3.5→3.66 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.5 / Num. unique all: 10849 / % possible all: 94
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 70.7 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 49.6 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 4

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: bovine glutamate dehydrogenase

Resolution: 3.5→19.97 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 3517 4 %RANDOM
Rwork0.207 ---
all0.23 90105 --
obs0.2071 87237 94 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.9046 Å2 / ksol: 0.230293 e/Å3
Displacement parametersBiso mean: 59.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.05 Å20 Å20 Å2
2---0.97 Å20 Å2
3----6.07 Å2
Refine analyzeLuzzati coordinate error free: 0.46 Å / Luzzati sigma a free: 0.59 Å
Refinement stepCycle: LAST / Resolution: 3.5→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46488 0 324 0 46812
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d1.27
X-RAY DIFFRACTIONc_mcbond_it7.251.5
X-RAY DIFFRACTIONc_mcangle_it10.732
X-RAY DIFFRACTIONc_scbond_it10.362
X-RAY DIFFRACTIONc_scangle_it13.962.5
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.336 520 3.9 %
Rwork0.251 12946 -
obs--88 %
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: 3.5 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.92
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.27
LS refinement shell
*PLUS
Rfactor Rfree: 0.35 / Rfactor Rwork: 0.264

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