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- PDB-2yfh: Structure of a Chimeric Glutamate Dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 2yfh
TitleStructure of a Chimeric Glutamate Dehydrogenase
ComponentsGLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / CHIMERA
Function / homology
Function and homology information


glutamate dehydrogenase complex / glutamate dehydrogenase (NADP+) / glutamate biosynthetic process / glutamate metabolic process / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / amino acid metabolic process / guanosine tetraphosphate binding / nucleotide binding / identical protein binding ...glutamate dehydrogenase complex / glutamate dehydrogenase (NADP+) / glutamate biosynthetic process / glutamate metabolic process / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / amino acid metabolic process / guanosine tetraphosphate binding / nucleotide binding / identical protein binding / cytoplasm / 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 / Glu/Leu/Phe/Val 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
Glutamate dehydrogenase / NADP-specific glutamate dehydrogenase
Similarity search - Component
Biological speciesCLOSTRIDIUM SYMBIOSUM (bacteria)
ESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.695 Å
AuthorsOliveira, T. / Panjikar, S. / Sharkey, M.A. / Carrigan, J.B. / Hamza, M. / Engel, P.C. / Khan, A.R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal Structure of a Chimaeric Bacterial Glutamate Dehydrogenase.
Authors: Oliveira, T. / Sharkey, M.A. / Engel, P.C. / Khan, A.R.
History
DepositionApr 5, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jun 29, 2016Group: Database references
Revision 1.3Mar 15, 2017Group: Source and taxonomy
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE
B: GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE
C: GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE
D: GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE
E: GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE
F: GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)290,5796
Polymers290,5796
Non-polymers00
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24680 Å2
ΔGint-53 kcal/mol
Surface area87360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.102, 113.859, 109.581
Angle α, β, γ (deg.)116.54, 101.54, 104.09
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE


Mass: 48429.789 Da / Num. of mol.: 6 / Fragment: RESIDUES 1-200,202-405,407-450
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM SYMBIOSUM (bacteria), (gene. exp.) ESCHERICHIA COLI (E. coli)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): DELTA GDHA
References: UniProt: E7GGS1, UniProt: P00370, glutamate dehydrogenase (NADP+), glutamate dehydrogenase [NAD(P)+], glutamate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 3.41 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growpH: 7
Details: 1.4 M AMMONIUM SULFATE, 0.1 M TRIS-HCL PH 6.5-8, 10% DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→36.5 Å / Num. obs: 108370 / % possible obs: 94.1 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 55.84 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.8
Reflection shellResolution: 2.7→2.79 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.6 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BGV

1bgv


Resolution: 2.695→36.524 Å / SU ML: 0.41 / σ(F): 1.96 / Phase error: 32.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2823 5045 5 %
Rwork0.215 --
obs0.2184 101418 93.62 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.177 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso mean: 72.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.1209 Å2-17.4733 Å2-6.4074 Å2
2---0.1842 Å28.0269 Å2
3---2.3051 Å2
Refinement stepCycle: LAST / Resolution: 2.695→36.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20327 0 0 313 20640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00820733
X-RAY DIFFRACTIONf_angle_d1.29528022
X-RAY DIFFRACTIONf_dihedral_angle_d17.1767524
X-RAY DIFFRACTIONf_chiral_restr0.0883016
X-RAY DIFFRACTIONf_plane_restr0.0053710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6951-2.79130.39164610.30439213X-RAY DIFFRACTION89
2.7913-2.90310.36715010.29679957X-RAY DIFFRACTION97
2.9031-3.03510.35775400.268710073X-RAY DIFFRACTION98
3.0351-3.19510.33415510.253710050X-RAY DIFFRACTION98
3.1951-3.39510.29185300.232910049X-RAY DIFFRACTION98
3.3951-3.6570.27935410.22069879X-RAY DIFFRACTION96
3.657-4.02460.29324950.19979691X-RAY DIFFRACTION94
4.0246-4.6060.2344490.17779084X-RAY DIFFRACTION88
4.606-5.79930.26155180.18889359X-RAY DIFFRACTION91
5.7993-36.52720.24874590.20139018X-RAY DIFFRACTION87

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