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- PDB-2zho: Crystal structure of the regulatory subunit of aspartate kinase f... -

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Basic information

Entry
Database: PDB / ID: 2zho
TitleCrystal structure of the regulatory subunit of aspartate kinase from Thermus thermophilus (ligand free form)
ComponentsAspartokinase
KeywordsTRANSFERASE / regulatory domain / ACT domain / Alternative initiation / Amino-acid biosynthesis / Diaminopimelate biosynthesis / Kinase / Lysine biosynthesis
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 / ACT domain / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / : / ACT domain / Aspartokinase signature. / ACT domain / ACT domain ...Aspartokinase catalytic domain / ACT domain / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / : / ACT domain / Aspartokinase signature. / ACT domain / 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
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsYoshida, A. / Tomita, T. / Kuzuyama, T. / Nishiyama, M.
Citation
Journal: Febs J. / Year: 2009
Title: Crystal structures of the regulatory subunit of Thr-sensitive aspartate kinase from Thermus thermophilus
Authors: Yoshida, A. / Tomita, T. / Kono, H. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M.
#1: Journal: J.Biosci.Bioeng. / Year: 1999
Title: Kinetic and mutation analyses of aspartate kinase from Thermus flavus
Authors: Kobashi, N. / Nishiyama, M. / Tanokura, M.
#2: Journal: Microbiology / Year: 1995
Title: An operon encoding aspartokinase and purine phosphoribosyltransferase in Thermus flavus
Authors: Nishiyama, M. / Kukimoto, M. / Beppu, T. / Horinouchi, S.
History
DepositionFeb 6, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartokinase
B: Aspartokinase
C: Aspartokinase
D: Aspartokinase
E: Aspartokinase
F: Aspartokinase


Theoretical massNumber of molelcules
Total (without water)106,4306
Polymers106,4306
Non-polymers00
Water1,42379
1
A: Aspartokinase
B: Aspartokinase


Theoretical massNumber of molelcules
Total (without water)35,4772
Polymers35,4772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-23 kcal/mol
Surface area12500 Å2
MethodPISA
2
C: Aspartokinase
D: Aspartokinase


Theoretical massNumber of molelcules
Total (without water)35,4772
Polymers35,4772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-25 kcal/mol
Surface area12490 Å2
MethodPISA
3
E: Aspartokinase
F: Aspartokinase


Theoretical massNumber of molelcules
Total (without water)35,4772
Polymers35,4772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-24 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.179, 107.179, 87.219
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Aspartokinase / Aspartate kinase


Mass: 17738.367 Da / Num. of mol.: 6
Fragment: regulatory subunit, Aspartokinase subunit alpha and beta, UNP residues 245-405
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: AT-62 / Gene: ask / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: P61489, aspartate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.6M sodium chloride, 0.1M Sodium citrate, 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: Jun 1, 2006 / Details: mirror
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.98→46.41 Å / Num. all: 22878 / Num. obs: 22878 / % possible obs: 99.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 67.7 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 21
Reflection shellResolution: 2.98→3.09 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3.23 / Rsym value: 0.371 / % possible all: 100

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Processing

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

2dt9


Resolution: 2.98→46.41 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2406887.39 / 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
Rfree0.266 1151 5 %RANDOM
Rwork0.244 ---
obs0.244 22812 99.6 %-
all-22878 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.2789 Å2 / ksol: 0.309011 e/Å3
Displacement parametersBiso mean: 56.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å27.67 Å20 Å2
2---0.06 Å20 Å2
3---0.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.98→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6453 0 0 79 6532
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d1.76
LS refinement shellResolution: 2.98→3.17 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 196 5.2 %
Rwork0.31 3575 -
obs--98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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