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- PDB-1bgv: GLUTAMATE DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1bgv
TitleGLUTAMATE DEHYDROGENASE
ComponentsGLUTAMATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


L-glutamate catabolic process via 2-hydroxyglutarate / glutamate dehydrogenase / glutamate biosynthetic process / glutamate dehydrogenase (NAD+) activity / glutamate dehydrogenase (NADP+) activity / amino acid metabolic process / cytosol
Similarity search - Function
Glutamate Dehydrogenase, chain A, domain 3 / Glutamate Dehydrogenase; Chain A, domain 3 / : / 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 ...Glutamate Dehydrogenase, chain A, domain 3 / Glutamate Dehydrogenase; Chain A, domain 3 / : / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / NAD-specific glutamate dehydrogenase
Similarity search - Component
Biological speciesClostridium symbiosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsStillman, T.J. / Baker, P.J. / Britton, K.L. / Rice, D.W.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis.
Authors: Stillman, T.J. / Baker, P.J. / Britton, K.L. / Rice, D.W.
#1: Journal: Biochemistry / Year: 1997
Title: Determinants of Substrate Specificity in the Superfamily of Amino Acid Dehydrogenases
Authors: Baker, P.J. / Waugh, M.L. / Wang, X.G. / Stillman, T.J. / Turnbull, A.P. / Engel, P.C. / Rice, D.W.
#2: Journal: Structure / Year: 1995
Title: The Structure of Pyrococcus Furiosus Glutamate Dehydrogenase Reveals a Key Role for Ion-Pair Networks in Maintaining Enzyme Stability at Extreme Temperatures
Authors: Yip, K.S. / Stillman, T.J. / Britton, K.L. / Artymiuk, P.J. / Baker, P.J. / Sedelnikova, S.E. / Engel, P.C. / Pasquo, A. / Chiaraluce, R. / Consalvi, V. / Scandurra, R. / Rice, D.W.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: Erratum. Structural Consequences of Sequence Patterns in the Fingerprint Region of the Nucleotide Binding Fold. Implications for Nucleotide Specificity
Authors: Baker, P.J. / Britton, K.L. / Rice, D.W. / Rob, A. / Stillman, T.J.
#4: Journal: J.Mol.Biol. / Year: 1992
Title: Structural Consequences of Sequence Patterns in the Fingerprint Region of the Nucleotide Binding Fold. Implications for Nucleotide Specificity
Authors: Baker, P.J. / Britton, K.L. / Rice, D.W. / Rob, A. / Stillman, T.J.
#5: Journal: Proteins / Year: 1992
Title: Subunit Assembly and Active Site Location in the Structure of Glutamate Dehydrogenase
Authors: Baker, P.J. / Britton, K.L. / Engel, P.C. / Farrants, G.W. / Lilley, K.S. / Rice, D.W. / Stillman, T.J.
#6: Journal: Eur.J.Biochem. / Year: 1992
Title: Structural Relationship between the Hexameric and Tetrameric Family of Glutamate Dehydrogenases
Authors: Britton, K.L. / Baker, P.J. / Rice, D.W. / Stillman, T.J.
#7: Journal: J.Mol.Biol. / Year: 1985
Title: Crystallization of an Nad+-Dependent Glutamate Dehydrogenase from Clostridium Symbiosum
Authors: Rice, D.W. / Hornby, D.P. / Engel, P.C.
History
DepositionJun 1, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3632
Polymers49,2161
Non-polymers1471
Water3,909217
1
A: GLUTAMATE DEHYDROGENASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)296,17712
Polymers295,2946
Non-polymers8836
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area23830 Å2
ΔGint-46 kcal/mol
Surface area85680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)162.800, 162.800, 102.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein GLUTAMATE DEHYDROGENASE


Mass: 49215.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THE RESIDUE LABELLED B 501, A GLUTAMATE, IS THE ENZYME'S SUBSTRATE WHICH IS BOUND WITHIN THE ACTIVE SITE. IT IS THOUGHT TO AN ONLY PARTIALLY OCCUPIED SITE AND SO ITS OCCUPANCY WAS SET TO 0.53.
Source: (natural) Clostridium symbiosum (bacteria) / References: UniProt: P24295, glutamate dehydrogenase
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 54 %
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.88
DetectorDetector: FILM / Date: Oct 7, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 42325 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.36 % / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
PHASEmodel building
TNT5Erefinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→10 Å / Isotropic thermal model: TNT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: THE RESIDUE LABELLED B 501, A GLUTAMATE, IS THE ENZYME'S SUBSTRATE WHICH IS BOUND WITHIN THE ACTIVE SITE. IT IS THOUGHT TO AN ONLY PARTIALLY OCCUPIED SITE AND SO ITS OCCUPANCY WAS SET TO 0.53.
RfactorNum. reflection% reflection
Rwork0.173 --
all0.173 40005 -
obs-40005 99 %
Solvent computationSolvent model: MOEWS AND KRETSINGER / Bsol: 248 Å2 / ksol: 0.85 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3460 0 10 217 3687
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01735434
X-RAY DIFFRACTIONt_angle_deg1.72347714
X-RAY DIFFRACTIONt_dihedral_angle_d16.85721130
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.017976
X-RAY DIFFRACTIONt_gen_planes0.01951715
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.283360.5

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