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- PDB-1v9l: L-glutamate dehydrogenase from Pyrobaculum islandicum complexed w... -

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Basic information

Entry
Database: PDB / ID: 1v9l
TitleL-glutamate dehydrogenase from Pyrobaculum islandicum complexed with NAD
Componentsglutamate dehydrogenase
KeywordsOXIDOREDUCTASE / Protein-NAD complex
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor / amino acid metabolic process / nucleotide binding
Similarity search - Function
Glutamate dehydrogenase / Leucine Dehydrogenase, chain A, domain 1 / NAD(P) binding domain of glutamate dehydrogenase / 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 ...Glutamate dehydrogenase / Leucine Dehydrogenase, chain A, domain 1 / NAD(P) binding domain of glutamate dehydrogenase / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glutamate dehydrogenase
Similarity search - Component
Biological speciesPyrobaculum islandicum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsBhuiya, M.W. / Sakuraba, H. / Ohshima, T. / Imagawa, T. / Katunuma, N. / Tsuge, H.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: The First Crystal Structure of Hyperthermostable NAD-dependent Glutamate Dehydrogenase from Pyrobaculum islandicum
Authors: Bhuiya, M.W. / Sakuraba, H. / Ohshima, T. / Imagawa, T. / Katunuma, N. / Tsuge, H.
#1: Journal: Appl.Environ.Microbiol. / Year: 1998
Title: Enzymological characteristics of the hyperthermostable NAD-dependent glutamate dehydrogenase from the archaeon Pyrobaculum islandicum and effects of denaturants and organic solvents
Authors: Kujo, C. / Ohshima, T.
History
DepositionJan 26, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2004Provider: 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,75312
Polymers281,7736
Non-polymers3,9816
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21410 Å2
ΔGint-94 kcal/mol
Surface area88270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.210, 165.880, 181.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
glutamate dehydrogenase / Hyperthermostable NAD-dependent L-glutamate dehydrogenase


Mass: 46962.086 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum islandicum (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y8I4, glutamate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG MME 550, Sodium chloride, NAD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
ROTATING ANODE21.5418
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.54181
ReflectionResolution: 2.8→50 Å / Num. all: 70811 / % possible obs: 93 %
Reflection shellResolution: 2.8→2.9 Å / % possible all: 93

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 2.8→50 Å
RfactorNum. reflection
Rfree0.26 -
Rwork0.2 -
all0.206 61142
obs0.206 287706
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19693 0 264 130 20087

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