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- PDB-1k89: K89L MUTANT OF GLUTAMATE DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1k89
TitleK89L MUTANT OF GLUTAMATE 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
NAD-specific glutamate dehydrogenase
Similarity search - Component
Biological speciesClostridium symbiosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsStillman, T.J. / Migueis, A.M.B. / Wang, X.G. / Baker, P.J. / Britton, K.L. / Engel, P.C. / Rice, D.W.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Insights into the mechanism of domain closure and substrate specificity of glutamate dehydrogenase from Clostridium symbiosum.
Authors: Stillman, T.J. / Migueis, A.M. / Wang, X.G. / Baker, P.J. / Britton, K.L. / Engel, P.C. / 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.
#3: 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.
#4: 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.
#5: 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.
#6: 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.
#7: 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.
History
DepositionJun 5, 1998Processing site: BNL
Revision 1.0Jan 27, 1999Provider: 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 3, 2021Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / software / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAMATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)49,2001
Polymers49,2001
Non-polymers00
Water4,288238
1
A: GLUTAMATE DEHYDROGENASE
x 6


Theoretical massNumber of molelcules
Total (without water)295,1986
Polymers295,1986
Non-polymers00
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 area23850 Å2
ΔGint-41 kcal/mol
Surface area85830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)161.800, 161.800, 102.500
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: 49199.625 Da / Num. of mol.: 1 / Mutation: K89L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium symbiosum (bacteria) / Gene: GDH / Plasmid: PTAC85-PTAC44 / Gene (production host): GDH / Production host: Escherichia coli (E. coli) / Strain (production host): Q100 / References: UniProt: P24295, glutamate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.6 Å3/Da / Density % sol: 53.11 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
20.25 Msodium glutamate1drop
30.1 Msodium phosphate1drop
41 mMbeta-mercaptoethanol1drop
51 mMEDTA1drop
639.5-40.5 %satammonium sulfate1reservoir

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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 / Date: Nov 23, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.05→24 Å / Num. obs: 27219 / % possible obs: 84.7 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.029 / Net I/σ(I): 17.6
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.112 / Mean I/σ(I) obs: 6.4 / % possible all: 72.7
Reflection
*PLUS
Num. measured all: 97593
Reflection shell
*PLUS
% possible obs: 72.7 %

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Processing

Software
NameVersionClassification
TFFCmodel building
TNT5Erefinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TFFCphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CLOSTRIDIUM SYMBIOSUM GLUTAMATE DEHYDROGENASE (WILD TYPE) CRYSTALLISED WITH SODIUM GLUTAMATE IN SPACE GROUP R32. ALL WATERS AND THE BOUND GLUTAMATE SUBSTRATE REMOVED.

Resolution: 2.05→10 Å / Isotropic thermal model: TNT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
all0.143 27063 -
obs-27063 83 %
Solvent computationSolvent model: MOEWS AND KRETSINGER / Bsol: 282 Å2 / ksol: 0.85 e/Å3
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3457 0 0 238 3695
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01635334
X-RAY DIFFRACTIONt_angle_deg1.63947614
X-RAY DIFFRACTIONt_dihedral_angle_d17.21521080
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.015957
X-RAY DIFFRACTIONt_gen_planes0.01751720
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.292440.5
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.149
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.07
X-RAY DIFFRACTIONt_angle_deg2.2
X-RAY DIFFRACTIONt_dihedral_angle_d0.008
X-RAY DIFFRACTIONt_plane_restr0.012

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