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- PDB-1gtm: STRUCTURE OF GLUTAMATE DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1gtm
TitleSTRUCTURE OF GLUTAMATE DEHYDROGENASE
ComponentsGLUTAMATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NAD / NADP
Function / homology
Function and homology information


glutamate dehydrogenase [NAD(P)+] activity / glutamate dehydrogenase [NAD(P)+] / amino acid metabolic process / cytoplasm
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 / 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 speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsYip, K.S.P. / Stillman, T.J. / Britton, K.L. / Pasquo, A. / 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: Eur.J.Biochem. / Year: 1995
Title: Insights Into Thermal Stability from a Comparison of the Glutamate Dehydrogenases from Pyrococcus Furiosus and Thermococcus Litoralis
Authors: Britton, K.L. / Baker, P.J. / Borges, K.M. / Engel, P.C. / Pasquo, A. / Rice, D.W. / Robb, F.T. / Scandurra, R. / Stillman, T.J. / Yip, K.S.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Crystallisation of the Nad(P)-Dependent Glutamate Dehydrogenase from the Hyperthermophile Pyrococcus Furiosus
Authors: Yip, K.S.P. / Stillman, T.J. / Baker, P.J. / Britton, K.L. / Engel, P.C. / Sedelnikova, S.E. / Rice, D.W. / Pasquo, A. / Chiaraluce, R. / Consalvi, V. / Scandurra, R.
History
DepositionAug 22, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 22, 2012Group: Database references
Revision 1.4Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details / _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
B: GLUTAMATE DEHYDROGENASE
C: GLUTAMATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,5249
Polymers140,9483
Non-polymers5766
Water5,729318
1
A: GLUTAMATE DEHYDROGENASE
B: GLUTAMATE DEHYDROGENASE
C: GLUTAMATE DEHYDROGENASE
hetero molecules

A: GLUTAMATE DEHYDROGENASE
B: GLUTAMATE DEHYDROGENASE
C: GLUTAMATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,04818
Polymers281,8966
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area22640 Å2
ΔGint-146 kcal/mol
Surface area82720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)167.200, 167.200, 172.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.50089, 0.86548, 0.00686), (-0.8655, -0.50091, 0.00069), (0.00403, -0.0056, 0.99998)27.67678, 105.15264, 0.03563
2given(-0.50089, 0.86548, 0.00686), (-0.8655, -0.50091, 0.00069), (0.00403, -0.0056, 0.99998)27.67678, 105.15264, 0.03563
3given(-0.51384, 0.85788, 0.0039), (-0.85789, -0.51383, -0.00223), (0.0001, -0.00449, 0.99999)29.01377, 105.30554, 0.24958
4given(-0.50003, -0.86601, 0.00212), (0.86597, -0.50003, -0.00784), (0.00785, -0.00208, 0.99997)105.03652, 28.87321, -0.28783
5given(-0.50003, -0.86601, 0.00212), (0.86597, -0.50003, -0.00784), (0.00785, -0.00208, 0.99997)105.03652, 28.87321, -0.28783
6given(-0.49593, -0.86833, 0.00823), (0.86836, -0.49594, 0.0001), (0.004, 0.00719, 0.99997)104.48633, 28.17576, -0.45124

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Components

#1: Protein GLUTAMATE DEHYDROGENASE /


Mass: 46982.590 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / Strain: DSM 3638
References: UniProt: P80319, glutamate dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / 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: 4.28 Å3/Da / Density % sol: 67.4 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 290 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: Yip, K.S.P., (1995) Acta Crystallogr.,Sect.D, 51, 240.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.5-2.7 Mlithium sulfate1drop
30.1 MHEPES1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionNum. obs: 115181 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.043
Reflection
*PLUS
Highest resolution: 2.2 Å / Redundancy: 2.58 %

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Processing

Software
NameClassification
TNTrefinement
MOSFLMdata reduction
RefinementResolution: 2.2→10 Å
RfactorNum. reflection% reflection
Rwork0.174 --
obs-113882 93.2 %
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9876 0 30 318 10224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg2.843
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
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 115153 / Rfactor obs: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38 Å2
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.85

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