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- PDB-2tmg: THERMOTOGA MARITIMA GLUTAMATE DEHYDROGENASE MUTANT S128R, T158E, ... -

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Basic information

Entry
Database: PDB / ID: 2tmg
TitleTHERMOTOGA MARITIMA GLUTAMATE DEHYDROGENASE MUTANT S128R, T158E, N117R, S160E
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 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKnapp, S. / Lebbink, J.H.G. / van der Oost, J. / de Vos, W.M. / Rice, D. / Ladenstein, R.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Engineering activity and stability of Thermotoga maritima glutamate dehydrogenase. II: construction of a 16-residue ion-pair network at the subunit interface.
Authors: Lebbink, J.H. / Knapp, S. / van der Oost, J. / Rice, D. / Ladenstein, R. / de Vos, W.M.
History
DepositionDec 4, 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: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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)275,4696
Polymers275,4696
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16900 Å2
ΔGint-41 kcal/mol
Surface area88060 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:
IDCodeMatrixVector
1given(0.391625, 0.11114, 0.913388), (0.910646, -0.188939, -0.367459), (0.131735, 0.975679, -0.175202)-83.78306, 95.64513, 47.35187
2given(0.383697, 0.914318, 0.12961), (0.123641, -0.189954, 0.973977), (0.915144, -0.357687, -0.185932)-22.08103, 111.83758, -73.21703
3given(-0.362132, -0.136256, -0.922114), (-0.190422, -0.957581, 0.21628), (-0.912469, 0.253913, 0.320825)65.9028, 195.07599, 11.08525
4given(-0.999373, 0.035166, -0.004182), (0.002438, -0.049481, -0.998772), (-0.035329, -0.998156, 0.049364)37.77623, 128.54166, 123.70579
5given(-0.397986, -0.911586, -0.103045), (-0.913913, 0.384196, 0.130979), (-0.079809, 0.146302, -0.986015)120.8998, 75.74597, 34.64244

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Components

#1: Protein
PROTEIN (GLUTAMATE DEHYDROGENASE)


Mass: 45911.531 Da / Num. of mol.: 6 / Mutation: S128R, T158E, N117R, S160E
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: 59.07 %
Crystal growpH: 6.5
Details: 6% POLYETHYLENE GLYCOLE, 120 MM AMMONIUM ACETATE, 50 MM BIS-TRIS PROPANE PH 6.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14-6 %(v/v)PEG11
2120 mMammonium acetate11
350 mMBis-Tris propane11

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.013
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.013 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 72518 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.07 / Rsym value: 0.045
Reflection shellResolution: 2.9→3 Å / % possible all: 97.1
Reflection
*PLUS
Num. measured all: 153233
Reflection shell
*PLUS
% possible obs: 97.1 %

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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: 2.9→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.274 -10 %RANDOM
Rwork0.211 ---
obs0.211 72518 98 %-
Displacement parametersBiso mean: 47 Å2
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19032 0 0 0 19032
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg0.906
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.537
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_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.537

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