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- PDB-2dtj: Crystal structure of regulatory subunit of aspartate kinase from ... -

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Basic information

Entry
Database: PDB / ID: 2dtj
TitleCrystal structure of regulatory subunit of aspartate kinase from Corynebacterium glutamicum
ComponentsAspartokinase
KeywordsTRANSFERASE / protein-ligand complex / regulatory subunit
Function / homology
Function and homology information


aspartate kinase / aspartate kinase activity / homoserine biosynthetic process / threonine biosynthetic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / ATP binding / cytosol
Similarity search - Function
Aspartokinase catalytic domain / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / : / ACT domain / Aspartokinase signature. / ACT domain / ACT domain profile. / ACT domain ...Aspartokinase catalytic domain / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / : / ACT domain / Aspartokinase signature. / ACT domain / ACT domain profile. / ACT domain / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / ACT-like domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / THREONINE / Aspartokinase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsYoshida, A. / Tomita, T. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Structural Insight into Concerted Inhibition of alpha(2)beta(2)-Type Aspartate Kinase from Corynebacterium glutamicum
Authors: Yoshida, A. / Tomita, T. / Kurihara, T. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M.
#1: Journal: APPL.MICROBIOL.BIOTECHNOL. / Year: 1990
Title: Cloning of a DNA fragment from Corynebacterium glutamicum conferring aminoethyl cysteine resistance and feedback resistance to aspartokinase
Authors: Thierbach, G. / Kalinowski, J. / Bachmann, B. / Puhler, A.
#2: Journal: MOL.MICROBIOL. / Year: 1991
Title: Genetic and biochemical analysis of the aspartokinase from Corynebacterium glutamicum
Authors: Kalinowski, J. / Cremer, J. / Bachmann, B. / Eggeling, L. / Sahm, H. / Puhler, A.
#3: Journal: Biochem.Biophys.Res.Commun. / Year: 2004
Title: Conversion of feedback regulation in aspartate kinase by domain exchange
Authors: Kato, C. / Kurihara, T. / Kobashi, N. / Yamane, H. / Nishiyama, M.
History
DepositionJul 12, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartokinase
B: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2005
Polymers38,7702
Non-polymers4303
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-17 kcal/mol
Surface area13510 Å2
MethodPISA
2
A: Aspartokinase
B: Aspartokinase
hetero molecules

A: Aspartokinase
B: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,40010
Polymers77,5394
Non-polymers8616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12460 Å2
ΔGint-47 kcal/mol
Surface area24980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.989, 59.010, 75.782
Angle α, β, γ (deg.)90.00, 116.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-510-

HOH

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Components

#1: Protein Aspartokinase


Mass: 19384.752 Da / Num. of mol.: 2
Fragment: regulatory subunit, Aspartokinase alpha subunit and Aspartokinase beta subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Plasmid: PET26B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon plus RIL / References: UniProt: P26512, aspartate kinase
#2: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO3
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.2M Ammonium Sulfate, 0.1M Citrate, 36 %(w/v) PEG 4000, 10mM threonine, pH 5.0, 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: Jan 28, 2006 / Details: mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. all: 43305 / Num. obs: 43305 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 24.5
Reflection shellResolution: 1.58→1.64 Å / Mean I/σ(I) obs: 3.5 / % possible all: 97.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DT9

2dt9


Resolution: 1.58→35.87 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1384008.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2121 4.9 %RANDOM
Rwork0.195 ---
obs0.195 42976 98.9 %-
all-43305 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.8861 Å2 / ksol: 0.37687 e/Å3
Displacement parametersBiso mean: 19.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å21.5 Å2
2--0.73 Å20 Å2
3---0.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.58→35.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2471 0 29 275 2775
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.027
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.62
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.11.5
X-RAY DIFFRACTIONc_mcangle_it2.912
X-RAY DIFFRACTIONc_scbond_it3.712
X-RAY DIFFRACTIONc_scangle_it4.972.5
LS refinement shellResolution: 1.58→1.68 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 363 5.3 %
Rwork0.231 6542 -
obs--96.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2Thr.paramThr.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4citrate2.paramcitrate2.top

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