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- PDB-8kao: Glutamate dehydrogenase-69O -

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Basic information

Entry
Database: PDB / ID: 8kao
TitleGlutamate dehydrogenase-69O
ComponentsGlutamate dehydrogenase
KeywordsOXIDOREDUCTASE / glutamate dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor / amino acid metabolic process / nucleotide binding
Similarity search - Function
Glutamate dehydrogenase / 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 ...Glutamate dehydrogenase / 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 domain superfamily
Similarity search - Domain/homology
2-oxopentanoic acid / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glutamate dehydrogenase
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSakuraba, H. / Ohshima, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Structure of glutamate dehydrogenase-69O
Authors: Sakuraba, H. / Ohshima, T.
History
DepositionAug 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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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)137,4645
Polymers136,6843
Non-polymers7802
Water1,964109
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)274,92810
Polymers273,3696
Non-polymers1,5594
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area18320 Å2
ΔGint-44 kcal/mol
Surface area82130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.782, 153.599, 110.550
Angle α, β, γ (deg.)90.00, 115.58, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

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Components

#1: Protein Glutamate dehydrogenase


Mass: 45561.473 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (archaea) / Gene: HFC64_02080 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E3K1C8
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-69O / 2-oxopentanoic acid / 2-Ketopentanoic acid


Mass: 116.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Potassium phosphate monobasic/Sodium phosphate dibasic buffer (pH 6.2), 10% (w/v) polyethylene glycol (PEG) 3,000, and 10% (v/v) glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→45.04 Å / Num. obs: 48864 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.068 / Rrim(I) all: 0.18 / Χ2: 0.98 / Net I/σ(I): 10.3
Reflection shellResolution: 2.55→2.63 Å / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 1.164 / Num. measured all: 30810 / Num. unique obs: 4486 / CC1/2: 0.708 / Rpim(I) all: 0.476 / Rrim(I) all: 1.259 / Χ2: 1 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→45.04 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.902 / SU B: 11.32 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.55 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26022 2490 5.1 %RANDOM
Rwork0.20796 ---
obs0.21054 46373 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.374 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å2-0.43 Å2
2---3.39 Å20 Å2
3---3.37 Å2
Refinement stepCycle: 1 / Resolution: 2.55→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9180 0 52 109 9341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0129370
X-RAY DIFFRACTIONr_bond_other_d0.0480.0169056
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.63112659
X-RAY DIFFRACTIONr_angle_other_deg0.9811.56321043
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63551191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.747557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.984101688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.21465
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210577
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021746
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.575.0474788
X-RAY DIFFRACTIONr_mcbond_other3.5695.0474788
X-RAY DIFFRACTIONr_mcangle_it5.3597.565971
X-RAY DIFFRACTIONr_mcangle_other5.3597.565972
X-RAY DIFFRACTIONr_scbond_it3.9995.2974582
X-RAY DIFFRACTIONr_scbond_other3.9985.2974583
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1677.8116689
X-RAY DIFFRACTIONr_long_range_B_refined8.17762.86310592
X-RAY DIFFRACTIONr_long_range_B_other8.17762.86310591
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 187 -
Rwork0.281 3439 -
obs--100 %

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