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- PDB-6dqg: Human glutamate dehydrogenase, H454Y mutant -

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Basic information

Entry
Database: PDB / ID: 6dqg
TitleHuman glutamate dehydrogenase, H454Y mutant
ComponentsGlutamate dehydrogenase 1, mitochondrial
KeywordsOXIDOREDUCTASE / Glutamate / dehydrogenase / insulin / hyperinsulinism
Function / homology
Function and homology information


L-leucine binding / glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / glutamate biosynthetic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / Glutamate and glutamine metabolism / glutamine metabolic process ...L-leucine binding / glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / glutamate biosynthetic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / Glutamate and glutamine metabolism / glutamine metabolic process / NAD+ binding / substantia nigra development / ADP binding / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / mitochondrial matrix / GTP binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / ATP binding / cytoplasm
Similarity search - Function
Helix Hairpins - #140 / 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 ...Helix Hairpins - #140 / 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 / Helix Hairpins / 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
PHOSPHATE ION / Glutamate dehydrogenase 1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSmith, T.J.
CitationJournal: Proteins / Year: 2019
Title: Glutamate dehydrogenase: Structure of a hyperinsulinism mutant, corrections to the atomic model, and insights into a regulatory site.
Authors: Nassar, O.M. / Li, C. / Stanley, C.A. / Pettitt, B.M. / Smith, T.J.
History
DepositionJun 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate dehydrogenase 1, mitochondrial
B: Glutamate dehydrogenase 1, mitochondrial
C: Glutamate dehydrogenase 1, mitochondrial
D: Glutamate dehydrogenase 1, mitochondrial
E: Glutamate dehydrogenase 1, mitochondrial
F: Glutamate dehydrogenase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,24421
Polymers330,8206
Non-polymers1,42515
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36460 Å2
ΔGint-218 kcal/mol
Surface area103420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.803, 98.380, 124.300
Angle α, β, γ (deg.)85.940, 69.350, 61.000
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 10 - 505 / Label seq-ID: 1 - 496

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD
5chain EEE
6chain FFF

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Components

#1: Protein
Glutamate dehydrogenase 1, mitochondrial / / GDH 1


Mass: 55136.641 Da / Num. of mol.: 6 / Fragment: UNP residues 63-558 / Mutation: H454Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLUD1, GLUD / Production host: Escherichia coli (E. coli)
References: UniProt: P00367, glutamate dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: Reservoir: 10% w/v PEG8000, 0.1 M sodium chloride, 1.3% w/v octyl-b-glucopyranoside, 7.5% v/v MPD, 0.1 M sodium phosphate, pH 6.8, 1 mM sodium azide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5406 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.7→29.775 Å / Num. obs: 98035 / % possible obs: 95.9 % / Redundancy: 2.2 % / Net I/σ(I): 12.9
Reflection shellHighest resolution: 2.7 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→29.775 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 32.33
RfactorNum. reflection% reflection
Rfree0.2787 4607 5.07 %
Rwork0.2406 --
obs0.2425 90875 88.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.94 Å2 / Biso mean: 61.7848 Å2 / Biso min: 15.76 Å2
Refinement stepCycle: final / Resolution: 2.7→29.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23256 0 75 260 23591
Biso mean--66.92 45.24 -
Num. residues----2976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00823820
X-RAY DIFFRACTIONf_angle_d0.94932160
X-RAY DIFFRACTIONf_chiral_restr0.0513456
X-RAY DIFFRACTIONf_plane_restr0.0074188
X-RAY DIFFRACTIONf_dihedral_angle_d16.17514250
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3876X-RAY DIFFRACTIONPOSITIONAL0.064
12B3876X-RAY DIFFRACTIONPOSITIONAL0.064
13C3876X-RAY DIFFRACTIONPOSITIONAL0.071
14D3876X-RAY DIFFRACTIONPOSITIONAL0.052
15E3876X-RAY DIFFRACTIONPOSITIONAL0.058
16F3876X-RAY DIFFRACTIONPOSITIONAL0.056
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7001-2.73080.33251340.28622001213562
2.7308-2.76290.39741110.28922372248373
2.7629-2.79650.39751170.29332441255876
2.7965-2.83190.32911350.28062563269878
2.8319-2.86910.32631530.27062567272081
2.8691-2.90840.34861480.26772620276881
2.9084-2.94990.3051260.27372638276482
2.9499-2.99390.34831270.28052742286984
2.9939-3.04070.36291400.28472758289884
3.0407-3.09050.38211430.28392753289685
3.0905-3.14370.36031580.27162776293487
3.1437-3.20080.30981250.28092844296986
3.2008-3.26230.35361520.29232834298688
3.2623-3.32880.32281470.28332901304890
3.3288-3.40110.33671530.2732926307991
3.4011-3.48010.30291590.2713001316092
3.4801-3.5670.31821630.26873002316593
3.567-3.66320.27991420.25763043318593
3.6632-3.77080.28651560.24083022317894
3.7708-3.89230.2741630.25373083324694
3.8923-4.03110.27581560.24653047320395
4.0311-4.19210.2711600.24283085324596
4.1921-4.38230.2831790.23973124330396
4.3823-4.61250.25791770.2143111328897
4.6125-4.90030.24841950.21523134332997
4.9003-5.27680.26051770.21513151332897
5.2768-5.80420.27581900.23033165335598
5.8042-6.6360.23011690.22683181335099
6.636-8.33020.19831510.18793223337499
8.3302-29.77670.19532010.17643160336199

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