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- PDB-1bvu: GLUTAMATE DEHYDROGENASE FROM THERMOCOCCUS LITORALIS -

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Basic information

Entry
Database: PDB / ID: 1bvu
TitleGLUTAMATE DEHYDROGENASE FROM THERMOCOCCUS LITORALIS
ComponentsPROTEIN (GLUTAMATE DEHYDROGENASE)
KeywordsOXIDOREDUCTASE / Thermal Stability
Function / homology
Function and homology information


glutamate dehydrogenase [NAD(P)+] activity / glutamate dehydrogenase [NAD(P)+] / amino acid metabolic process / cytoplasm
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/phenylalanine/leucine/valine dehydrogenase, C-terminal ...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 / 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 speciesThermococcus litoralis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsBaker, P.J. / Britton, K.L. / Yip, K.S. / Stillman, T.J. / Rice, D.W.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Structure determination of the glutamate dehydrogenase from the hyperthermophile Thermococcus litoralis and its comparison with that from Pyrococcus furiosus
Authors: Britton, K.L. / Yip, K.S. / Sedelnikova, S.E. / Stillman, T.J. / Adams, M.W. / Ma, K. / Maeder, D.L. / Robb, F.T. / Tolliday, N. / Vetriani, C. / Rice, D.W. / Baker, P.J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Protein Thermostability Above 100C: A Key Role for Ionic Interactions
Authors: Vetriani, C. / Maeder, D.L. / Tolliday, N. / Yip, K.S.-P. / Stillman, T.J. / Britton, K.L. / Rice, D.W. / Klump, H.H. / Robb, F.T.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallisation of the Glutamate Dehydrogenase from the Hyperthermophilic Archaeon Thermococcus Litoralis
Authors: Sedelnikova, S.E. / Yip, K.S.-P. / Stillman, T.J. / Ma, K. / Adams, M.W.W. / Robb, F.T. / Rice, D.W.
History
DepositionJul 20, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (GLUTAMATE DEHYDROGENASE)
B: PROTEIN (GLUTAMATE DEHYDROGENASE)
C: PROTEIN (GLUTAMATE DEHYDROGENASE)
D: PROTEIN (GLUTAMATE DEHYDROGENASE)
E: PROTEIN (GLUTAMATE DEHYDROGENASE)
F: PROTEIN (GLUTAMATE DEHYDROGENASE)


Theoretical massNumber of molelcules
Total (without water)279,9856
Polymers279,9856
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.900, 197.500, 125.700
Angle α, β, γ (deg.)90.00, 113.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
PROTEIN (GLUTAMATE DEHYDROGENASE) / EC 1.4.1.3


Mass: 46664.219 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Thermococcus litoralis (archaea)
References: UniProt: Q56304, glutamate dehydrogenase [NAD(P)+]

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.33 %
Crystal growpH: 8
Details: 35MG/ML PROTEIN IN 0.1M HEPES BUFFER PH 8.0 CONTAINING 1.7-1.8M AMMONIUM SULPHATE AND 1.5% W/V PEG 8000.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
135 mg/mlprotein1drop
20.1 MHEPES1reservoir
31.7-1.8 Mammonium sulfate1reservoir
41.5 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 101702 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rmerge(I) obs: 0.042
Reflection
*PLUS
Num. measured all: 173711

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
MLPHAREphasing
TNTrefinement
CCP4(ROTAVATA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.5→10 Å / σ(F): 0 / Stereochemistry target values: PROTGEO /
Num. reflection% reflection
obs96460 87 %
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19566 0 0 0 19566
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
X-RAY DIFFRACTIONt_angle_deg1.53
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS

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