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- PDB-3aoe: Crystal structure of hetero-hexameric glutamate dehydrogenase fro... -

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Basic information

Entry
Database: PDB / ID: 3aoe
TitleCrystal structure of hetero-hexameric glutamate dehydrogenase from Thermus thermophilus (Leu bound form)
Components(Glutamate dehydrogenase) x 2
KeywordsOXIDOREDUCTASE / Rossmann fold / glutamate dehydrogenase / dehydrogenase / NADH
Function / homology
Function and homology information


glutamate dehydrogenase (NAD+) activity / L-glutamate catabolic process / nucleotide binding
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #1210 / 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 ...Helicase, Ruva Protein; domain 3 - #1210 / 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 / Helicase, Ruva Protein; domain 3 / 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
LEUCINE / Glutamate dehydrogenase / Glutamate dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsTomita, T. / Kuzuyama, T. / Nishiyama, M.
CitationJournal: To be Published
Title: An unique allosteric regulation revealed by hetero-hexameric glutamate dehydrogenase from Thermus thermophilus
Authors: Tomita, T. / Kuzuyama, T. / Nishiyama, M.
History
DepositionSep 27, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Mar 20, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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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
E: Glutamate dehydrogenase
F: Glutamate dehydrogenase
C: Glutamate dehydrogenase
D: Glutamate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,58512
Polymers270,7986
Non-polymers7876
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21720 Å2
ΔGint-93 kcal/mol
Surface area85490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.986, 146.093, 158.284
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutamate dehydrogenase


Mass: 46168.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: gdhB, TT_C1211 / Plasmid: pET-gdhA/gdhB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q72IC1, glutamate dehydrogenase [NAD(P)+]
#2: Protein
Glutamate dehydrogenase


Mass: 44615.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: gdhA, TT_C1212 / Plasmid: pET-gdhA/gdhB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q72IC0, glutamate dehydrogenase [NAD(P)+]
#3: Chemical
ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H13NO2 / Details: leucine
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate tribasic (pH5.6), 1.0M ammonium phosphate monobasic, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 29, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30.22 Å / Num. all: 87634 / Num. obs: 87634 / % possible obs: 99.9 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7
Reflection shellResolution: 2.6→2.64 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B26

1b26


Resolution: 2.6→30.22 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.901 / SU B: 24.844 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.944 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25961 4388 5 %RANDOM
Rwork0.19257 ---
obs0.19594 83048 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.615 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18973 0 54 312 19339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02219421
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.98226413
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00552510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24722.707820
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.798153081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1115196
X-RAY DIFFRACTIONr_chiral_restr0.1020.22974
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114906
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5931.512442
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.165219808
X-RAY DIFFRACTIONr_scbond_it1.92336979
X-RAY DIFFRACTIONr_scangle_it3.3074.56603
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.599→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 356 -
Rwork0.236 5973 -
obs--99.91 %
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)
10.5576-0.10850.25280.62340.07920.1113-0.03710.03370.1452-0.04-0.036-0.0726-0.01570.00110.0730.0135-0.0042-0.00580.03620.05770.116447.38451.03676.395
20.19630.09170.1860.45930.17560.6601-0.0110.08250.0215-0.07410.0211-0.04730.0341-0.0176-0.01010.0211-0.0220.00260.10880.03280.015552.089910.585-21.4635
30.3236-0.0581-0.1440.46720.1610.7556-0.0006-0.05840.01350.0565-0.03920.0182-0.0349-0.05050.03990.05-0.01180.00570.047-0.00620.01430.003125.952539.8222
40.5661-0.1465-0.05170.4479-0.06120.468-0.09320.1001-0.09390.01740.00170.04040.1268-0.15090.09150.0695-0.0720.03940.0845-0.03690.033124.5952-6.65748.5087
50.4630.4251-0.11340.41090.01680.58290.0201-0.07130.01030.0281-0.04020.0262-0.00180.08820.02010.02290.0111-0.00290.04920.01380.044174.63728.111233.4197
60.3117-0.189-0.1330.772-0.12290.2659-0.0311-0.0171-0.0478-0.00990.0142-0.02780.0479-0.00350.01690.0576-0.00490.00310.01660.02920.053668.7627-12.199713.2913
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 424
2X-RAY DIFFRACTION2B1 - 424
3X-RAY DIFFRACTION3E4 - 419
4X-RAY DIFFRACTION4F3 - 419
5X-RAY DIFFRACTION5C3 - 419
6X-RAY DIFFRACTION6D4 - 419

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