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- PDB-5ijz: Crystal structure of glutamate dehydrogenase(GDH) from Corynebact... -

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Basic information

Entry
Database: PDB / ID: 5ijz
TitleCrystal structure of glutamate dehydrogenase(GDH) from Corynebacterium glutamicum
ComponentsNADP-specific glutamate dehydrogenase
KeywordsOXIDOREDUCTASE / glutamate dehydrogenase
Function / homology
Function and homology information


glutamate dehydrogenase (NADP+) / glutamate biosynthetic process / glutamate dehydrogenase (NADP+) activity / cytoplasm
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 / 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
2-OXOGLUTARIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-specific glutamate dehydrogenase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsSon, H.-F. / Kim, K.-J.
CitationJournal: BIOCHEM.BIOPHYS.RES.COMMUN. / Year: 2015
Title: Structural insights into domain movement and cofactor specificity of glutamate dehydrogenase from Corynebacterium glutamicum
Authors: Son, H.-F. / Kim, K.-J.
History
DepositionMar 3, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Data collection / Derived calculations / Structure summary
Category: pdbx_prerelease_seq / pdbx_struct_oper_list / struct
Item: _pdbx_struct_oper_list.symmetry_operation / _struct.title
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADP-specific glutamate dehydrogenase
B: NADP-specific glutamate dehydrogenase
C: NADP-specific glutamate dehydrogenase
D: NADP-specific glutamate dehydrogenase
E: NADP-specific glutamate dehydrogenase
F: NADP-specific glutamate dehydrogenase
G: NADP-specific glutamate dehydrogenase
H: NADP-specific glutamate dehydrogenase
I: NADP-specific glutamate dehydrogenase
J: NADP-specific glutamate dehydrogenase
K: NADP-specific glutamate dehydrogenase
L: NADP-specific glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)596,55930
Polymers588,55312
Non-polymers8,00618
Water29,3461629
1
A: NADP-specific glutamate dehydrogenase
G: NADP-specific glutamate dehydrogenase
H: NADP-specific glutamate dehydrogenase
J: NADP-specific glutamate dehydrogenase
K: NADP-specific glutamate dehydrogenase
L: NADP-specific glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,83514
Polymers294,2776
Non-polymers3,5588
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31110 Å2
ΔGint-37 kcal/mol
Surface area80920 Å2
MethodPISA
2
B: NADP-specific glutamate dehydrogenase
C: NADP-specific glutamate dehydrogenase
D: NADP-specific glutamate dehydrogenase
E: NADP-specific glutamate dehydrogenase
F: NADP-specific glutamate dehydrogenase
I: NADP-specific glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,72416
Polymers294,2776
Non-polymers4,44810
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32710 Å2
ΔGint-37 kcal/mol
Surface area82780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.219, 93.032, 187.875
Angle α, β, γ (deg.)90.000, 108.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NADP-specific glutamate dehydrogenase / NADP-GDH


Mass: 49046.102 Da / Num. of mol.: 12 / Fragment: Substrate-binding domain (UNP RESIDUES 1-420)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: gdh, Cgl2079, cg2280 / Plasmid: pProEX-HTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-T1R
References: UniProt: P31026, glutamate dehydrogenase (NADP+)
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: C5H6O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1629 / 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: 2.42 Å3/Da / Density % sol: 49.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 3350, Tacsimate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 23, 2014
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.29→178.51 Å / Num. obs: 249267 / % possible obs: 98.6 % / Redundancy: 5.6 % / Net I/σ(I): 21.14
Reflection shellResolution: 2.3→2.34 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data collection
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BGV

1bgv


Resolution: 2.29→34.366 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.377 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.315 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 12145 4.9 %RANDOM
Rwork0.1646 ---
obs0.1674 233608 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 175.34 Å2 / Biso mean: 25.987 Å2 / Biso min: 5.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0 Å2-0.16 Å2
2---0.61 Å20 Å2
3---0.96 Å2
Refinement stepCycle: final / Resolution: 2.29→34.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40276 0 522 1632 42430
Biso mean--29.34 25.18 -
Num. residues----5221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01941644
X-RAY DIFFRACTIONr_bond_other_d0.0070.0238826
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.95956287
X-RAY DIFFRACTIONr_angle_other_deg1.076389215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69255207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41324.1011985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.878156853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.77715280
X-RAY DIFFRACTIONr_chiral_restr0.1060.25967
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0248088
X-RAY DIFFRACTIONr_gen_planes_other0.0020.029918
X-RAY DIFFRACTIONr_mcbond_it2.0742.46520870
X-RAY DIFFRACTIONr_mcbond_other2.0732.46520869
X-RAY DIFFRACTIONr_mcangle_it3.2753.68826063
LS refinement shellResolution: 2.293→2.353 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 765 -
Rwork0.203 14929 -
all-15694 -
obs--84.67 %

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