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- PDB-1hrd: GLUTAMATE DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1hrd
TitleGLUTAMATE DEHYDROGENASE
ComponentsGLUTAMATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NAD
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
NAD-specific glutamate dehydrogenase
Similarity search - Component
Biological speciesClostridium symbiosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.96 Å
AuthorsBritton, K.L. / Baker, P.J. / Stillman, T.J. / Rice, D.W.
Citation
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.
#1: 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.
#2: 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.
#3: 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.
#4: 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
DepositionApr 3, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 22, 2012Group: Database references
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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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


Theoretical massNumber of molelcules
Total (without water)147,6473
Polymers147,6473
Non-polymers00
Water9,386521
1
A: GLUTAMATE DEHYDROGENASE
B: GLUTAMATE DEHYDROGENASE
C: GLUTAMATE DEHYDROGENASE

A: GLUTAMATE DEHYDROGENASE
B: GLUTAMATE DEHYDROGENASE
C: GLUTAMATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)295,2946
Polymers295,2946
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area24400 Å2
ΔGint-55 kcal/mol
Surface area87960 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)147.100, 151.300, 94.600
Angle α, β, γ (deg.)90.00, 132.75, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-640-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.36524, -0.56404, 0.74058), (0.56311, -0.49962, -0.65824), (0.74128, 0.65745, 0.13513)-48.17755, 33.324, 56.2662
2given(0.3638, 0.56309, 0.74201), (-0.56347, -0.50128, 0.65667), (0.74172, -0.657, 0.13492)-42.93411, -47.48246, 50.01008
3given(0.3699, -0.52689, 0.76522), (0.59634, -0.49693, -0.63042), (0.71242, 0.68953, 0.13039)-49.73091, 32.26029, 55.64772
4given(0.39079, 0.5326, 0.75075), (-0.56601, -0.50414, 0.65228), (0.72589, -0.67984, 0.10445)-42.81768, -47.30594, 51.57361
5given(0.36098, -0.56035, 0.74546), (0.56937, -0.50065, -0.65206), (0.73858, 0.6598, 0.13834)-48.63605, 32.93981, 55.94542
6given(0.37088, 0.56017, 0.74072), (-0.56051, -0.50089, 0.65948), (0.74045, -0.65977, 0.12821)-42.81852, -47.64302, 50.44201

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Components

#1: Protein GLUTAMATE DEHYDROGENASE


Mass: 49215.648 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Clostridium symbiosum (bacteria) / Strain: HB25 / References: UniProt: P24295, glutamate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 45 %

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: FILM / Detector: FILM / Date: 1987
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionNum. obs: 96327 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.14

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Processing

Software
NameClassification
TNTrefinement
MOSFLMdata reduction
RefinementResolution: 1.96→37.8 Å / σ(F): 0
Details: TNT MEAN B (A**2) : 33.797 RMS CO-ORDINATE SHIFT IN FINAL CYCLE (A) : 0.008
RfactorNum. reflection% reflection
Rwork0.172 --
obs-96327 88 %
Refinement stepCycle: LAST / Resolution: 1.96→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10380 0 0 521 10901
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.893
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_planes0.018
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd

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