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- PDB-8kar: Glutamate dehydrogenase-AKG -

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Basic information

Entry
Database: PDB / ID: 8kar
TitleGlutamate dehydrogenase-AKG
ComponentsGlutamate dehydrogenase
KeywordsOXIDOREDUCTASE / Glutamate dehydrogenase
Function / homology
Function and homology information


glutamate dehydrogenase (NAD+) activity / L-glutamate catabolic 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-OXOGLUTARIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glutamate dehydrogenase
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsSakuraba, H. / Ohshima, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Extremophiles / Year: 2025
Title: Structural insight into the unique substrate specificity of glutamate dehydrogenase from Saccharolobus solfataricus.
Authors: Okabe, I. / Hirano, M. / Ohmori, T. / Segawa, M. / Yoneda, K. / Ohshima, T. / Sakuraba, H.
History
DepositionAug 3, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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)139,92022
Polymers136,6843
Non-polymers3,23519
Water7,530418
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)279,84044
Polymers273,3696
Non-polymers6,47138
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area18100 Å2
ΔGint-33 kcal/mol
Surface area82460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.267, 156.419, 99.330
Angle α, β, γ (deg.)90.00, 110.30, 90.00
Int Tables number5
Space group name H-MC121

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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-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.54 Å3/Da / Density % sol: 51.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES buffer (pH 6.5), 10% (w/v) PEG5,000 MME, 12% (v/v) 1-propanol, 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: Nov 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→47.21 Å / Num. obs: 141497 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.06 / Rrim(I) all: 0.156 / Χ2: 0.91 / Net I/σ(I): 7.8
Reflection shellResolution: 1.73→1.76 Å / % possible obs: 99.4 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.933 / Num. measured all: 37214 / Num. unique obs: 6919 / CC1/2: 0.789 / Rpim(I) all: 0.437 / Rrim(I) all: 1.034 / Χ2: 0.89 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→47.21 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 6.073 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23065 7121 5 %RANDOM
Rwork0.19655 ---
obs0.19826 134338 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.957 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20 Å20.59 Å2
2---1.58 Å20 Å2
3---1.96 Å2
Refinement stepCycle: 1 / Resolution: 1.73→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9480 0 214 418 10112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0129831
X-RAY DIFFRACTIONr_bond_other_d0.0450.0169437
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.63713277
X-RAY DIFFRACTIONr_angle_other_deg1.0421.5621935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37451239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.698560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.781101743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.21536
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211037
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021818
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_it1.6571.394965
X-RAY DIFFRACTIONr_mcbond_other1.6571.394965
X-RAY DIFFRACTIONr_mcangle_it2.4042.0796201
X-RAY DIFFRACTIONr_mcangle_other2.4042.0796202
X-RAY DIFFRACTIONr_scbond_it2.2031.6654866
X-RAY DIFFRACTIONr_scbond_other2.2031.6664867
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3272.3817077
X-RAY DIFFRACTIONr_long_range_B_refined4.7719.44911021
X-RAY DIFFRACTIONr_long_range_B_other4.73419.15610961
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 530 -
Rwork0.31 9837 -
obs--99.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.53030.46280.0710.43710.20480.67740.06060.01150.01420.0425-0.01470.0133-0.0592-0.0803-0.04580.0620.0267-0.0060.0517-0.00840.0716.312-3.929232.5588
20.1868-0.1207-0.00080.1092-0.04480.20170.01050.0559-0.00220.0163-0.0163-0.0204-0.0435-0.00260.00580.07410.0143-0.00260.06310.00840.050617.68695.066522.129
30.2721-0.09160.1340.4599-0.21350.15020.0410.1288-0.0752-0.0512-0.00630.02010.01720.0287-0.03480.06290.0286-0.02120.0995-0.02040.040313.1514-8.581514.0443
41.53570.0011-0.29240.00380.05691.0028-0.0758-0.1644-0.06130.01340.0002-0.00220.24550.00660.07560.07790.00390.03570.01920.01510.116334.2965-46.535838.7829
50.1658-0.0365-0.02730.29580.13350.13670.00570.0342-0.0019-0.0253-0.01950.0251-0.00790.0110.01370.07080.0026-0.00580.0475-0.00440.062326.6091-43.332122.8678
60.18850.13640.18130.33280.36970.48360.00810.13-0.0298-0.06030.1429-0.1558-0.11670.1899-0.1510.073-0.01780.03620.1077-0.03530.103745.1367-38.667720.1209
70.29150.4929-0.01991.83410.55160.3468-0.04330.05020.0873-0.21740.0450.1384-0.0942-0.0303-0.00180.07370.0158-0.03020.01680.00540.11384.5945-0.401849.3872
80.3047-0.1219-0.10730.4320.11970.0588-0.0297-0.0093-0.00770.04630.00310.10080.01860.01910.02650.04630.00730.01270.0477-0.00040.0985-1.2135-11.628962.4617
90.7250.4834-0.16830.47890.10060.3930.0963-0.22390.23180.0984-0.03960.10060.0510.1966-0.05670.07160.01040.00680.1338-0.09810.15349.66871.327171.8335
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 55
2X-RAY DIFFRACTION2A56 - 309
3X-RAY DIFFRACTION3A310 - 419
4X-RAY DIFFRACTION4B6 - 55
5X-RAY DIFFRACTION5B56 - 362
6X-RAY DIFFRACTION6B363 - 419
7X-RAY DIFFRACTION7C6 - 55
8X-RAY DIFFRACTION8C56 - 361
9X-RAY DIFFRACTION9C362 - 419

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