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- PDB-1b3b: THERMOTOGA MARITIMA GLUTAMATE DEHYDROGENASE MUTANT N97D, G376K -

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Basic information

Entry
Database: PDB / ID: 1b3b
TitleTHERMOTOGA MARITIMA GLUTAMATE DEHYDROGENASE MUTANT N97D, G376K
ComponentsPROTEIN (GLUTAMATE DEHYDROGENASE)
KeywordsOXIDOREDUCTASE / METABOLIC ROLE / GLUTAMATE / DEHYDROGENASE / MUTANT
Function / homology
Function and homology information


glutamate catabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity
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 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / 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 speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKnapp, S. / Lebbink, J.H.G. / Van Der Oost, J. / Devos, W.M. / Rice, D. / Ladenstein, R.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Engineering activity and stability of Thermotoga maritima glutamate dehydrogenase. I. Introduction of a six-residue ion-pair network in the hinge region.
Authors: Lebbink, J.H. / Knapp, S. / van der Oost, J. / Rice, D. / Ladenstein, R. / de Vos, W.M.
History
DepositionDec 7, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)274,8086
Polymers274,8086
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16300 Å2
ΔGint-61 kcal/mol
Surface area89480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.100, 145.100, 272.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.391625, 0.11114, 0.913388), (0.910646, -0.188939, -0.367459), (0.131735, 0.975679, -0.175202)
Vector: -83.78306, 95.64513, 47.35187)

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Components

#1: Protein
PROTEIN (GLUTAMATE DEHYDROGENASE)


Mass: 45801.395 Da / Num. of mol.: 6 / Mutation: N97D, G376K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Cellular location: CYTOPLASM / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3
References: UniProt: P96110, glutamate dehydrogenase [NAD(P)+]

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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: 3.1 Å3/Da / Density % sol: 59.16 %
Crystal growpH: 6.5
Details: 6% POLYETHYLENE GLYCOLE, 120 MM AMMONIUM ACETATE, 50 MM BIS-TRIS PROPANE PH 6.5
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlenzyme1drop
210 mMTris-HCl1drop
350 mMBis-Tris propane1reservoir
4120 mMammonium acetate1reservoir
53 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: NICKEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 53329 / % possible obs: 94 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.096 / Rsym value: 0.05
Reflection shellResolution: 3→3.14 Å / % possible all: 60
Reflection
*PLUS
Num. measured all: 151200
Reflection shell
*PLUS
% possible obs: 60 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→8 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.298 -10 %RANDOM
Rwork0.225 ---
obs0.225 53329 94 %-
Refinement stepCycle: LAST / Resolution: 3.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19008 0 0 0 19008
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.921
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.543
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.543

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