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- PDB-1b26: GLUTAMATE DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1b26
TitleGLUTAMATE DEHYDROGENASE
ComponentsGLUTAMATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / METABOLIC ROLE / GLUTAMATE / DEHYDROGENASE
Function / homology
Function and homology information


glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NAD+) activity / glutamate dehydrogenase (NADP+) activity / L-glutamate catabolic process
Similarity search - Function
: / Glutamate dehydrogenase / 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 dehydrogenase / 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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamate dehydrogenase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKnapp, S. / Devos, W.M. / Rice, D. / Ladenstein, R.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Crystal structure of glutamate dehydrogenase from the hyperthermophilic eubacterium Thermotoga maritima at 3.0 A resolution.
Authors: Knapp, S. / de Vos, W.M. / Rice, D. / Ladenstein, R.
History
DepositionDec 4, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 3, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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

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Assembly

Deposited unit
A: GLUTAMATE DEHYDROGENASE
B: GLUTAMATE DEHYDROGENASE
C: GLUTAMATE DEHYDROGENASE
D: GLUTAMATE DEHYDROGENASE
E: GLUTAMATE DEHYDROGENASE
F: GLUTAMATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)275,1576
Polymers275,1576
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16620 Å2
ΔGint-63 kcal/mol
Surface area89060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.130, 147.130, 273.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.390147, 0.123289, 0.912461), (0.910111, -0.201866, -0.361867), (0.139581, 0.971622, -0.190964)-84.33214, 97.14661, 47.7307
2given(0.390452, 0.913471, 0.11453), (0.140519, -0.182081, 0.973191), (0.909836, -0.36389, -0.199454)-23.98794, 112.0028, -73.09966
3given(-0.366049, -0.149459, -0.918515), (-0.185752, -0.955421, 0.229491), (-0.911868, 0.254621, 0.321968)66.98578, 196.69524, 10.38295
4given(-0.999198, 0.036121, -0.017263), (0.015359, -0.052322, -0.998512), (-0.03697, -0.997977, 0.051725)37.83105, 130.49754, 125.19853
5given(-0.405394, -0.908879, -0.097953), (-0.909577, 0.390353, 0.142454), (-0.091237, 0.146845, -0.984943)122.32049, 76.1136, 34.5845

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Components

#1: Protein
GLUTAMATE DEHYDROGENASE


Mass: 45859.473 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Cellular location: CYTOPLASM / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3
References: UniProt: P96110, 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: 3.1 Å3/Da / Density % sol: 60.4 %
Crystal growpH: 6.5
Details: CRYSTALLIZATION CONDITIONS: 3% POLYETHYLENE GLYCOLE, 120 MM AMMONIUM ACETATE 50 MM BIS-TRIS PROPANE PH 6.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 %PEG11
2120 mMammonium acetate11
350 mMBis-Tris propane11

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 57305 / % possible obs: 94 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.091 / Rsym value: 0.048
Reflection shellResolution: 3→3.1 Å / % possible all: 75
Reflection
*PLUS
Num. measured all: 220980
Reflection shell
*PLUS
% possible obs: 75 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.295 -10 %RANDOM
Rwork0.225 ---
obs-57305 94 %-
Displacement parametersBiso mean: 40.2 Å2
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18978 0 0 0 18978
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.032
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.14
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.058
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.14
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.058

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