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- PDB-2j0x: CRYSTAL STRUCTURE OF E. COLI ASPARTOKINASE III IN COMPLEX WITH LY... -

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Basic information

Entry
Database: PDB / ID: 2j0x
TitleCRYSTAL STRUCTURE OF E. COLI ASPARTOKINASE III IN COMPLEX WITH LYSINE AND ASPARTATE (T-STATE)
ComponentsLYSINE-SENSITIVE ASPARTOKINASE 3
KeywordsTRANSFERASE / FEEDBACK INHIBITION / ALLOSTERIC REGULATION / ASPARTOKINASE / ASPARTATE PATHWAY / LYSINE BIOSYNTHESIS / LYSINE / KINASE / ACT DOMAIN / AMINO ACID BIOSYNTHESIS / AMINO-ACID BIOSYNTHESIS
Function / homology
Function and homology information


aspartate kinase / aspartate kinase activity / homoserine biosynthetic process / lysine biosynthetic process via diaminopimelate / protein homodimerization activity / ATP binding / cytosol
Similarity search - Function
Lysine-sensitive aspartokinase 3, N-terminal catalytic domain / Aspartokinase, catalytic domain / Aspartokinase/Bifunctional aspartokinase/homoserine dehydrogenase, catalytic domain / : / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / : / ACT domain / Aspartokinase signature. ...Lysine-sensitive aspartokinase 3, N-terminal catalytic domain / Aspartokinase, catalytic domain / Aspartokinase/Bifunctional aspartokinase/homoserine dehydrogenase, catalytic domain / : / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / : / ACT domain / Aspartokinase signature. / ACT domain / ACT domain / Carbamate kinase / Acetylglutamate kinase-like / ACT domain profile. / ACT domain / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / ACT-like domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / LYSINE / PHOSPHATE ION / Lysine-sensitive aspartokinase 3
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKotaka, M. / Ren, J. / Lockyer, M. / Hawkins, A.R. / Stammers, D.K.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structures of R- and T-State Escherichia Coli Aspartokinase III: Mechanisms of the Allosteric Transition and Inhibition by Lysine.
Authors: Kotaka, M. / Ren, J. / Lockyer, M. / Hawkins, A.R. / Stammers, D.K.
History
DepositionAug 7, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 12-STRANDED BARREL THIS IS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LYSINE-SENSITIVE ASPARTOKINASE 3
B: LYSINE-SENSITIVE ASPARTOKINASE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,6816
Polymers97,1592
Non-polymers5224
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)171.750, 148.020, 42.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.1595, 0.9872, -0.0012), (0.9863, 0.1594, 0.0428), (0.0425, 0.0057, -0.9991)
Vector: 97.6, 177.5, 358.4)

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Components

#1: Protein LYSINE-SENSITIVE ASPARTOKINASE 3 / LYSINE-SENSITIVE ASPARTOKINASE III / ASPARTATE KINASE III


Mass: 48579.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET3D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08660, aspartate kinase
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growpH: 7
Details: 0.2M NA2 TARTRATE, 16-18% PEG3350, 0.1M TRIS PH 7.0, 2% MPD:ETHYLENE GLYCOL (1:1)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 3, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 26519 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.3 / % possible all: 87.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LOWER RESOLUTION (3A) STRUCTURE DETERMINED BY MAD PHASING

Resolution: 2.8→29.73 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1409946.37 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1278 4.8 %RANDOM
Rwork0.215 ---
obs0.215 26487 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.3125 Å2 / ksol: 0.336714 e/Å3
Displacement parametersBiso mean: 39.8 Å2
Baniso -1Baniso -2Baniso -3
1--15.44 Å20 Å20 Å2
2--1.01 Å20 Å2
3---14.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6781 0 34 100 6915
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.554
X-RAY DIFFRACTIONc_mcangle_it8.416
X-RAY DIFFRACTIONc_scbond_it9.288
X-RAY DIFFRACTIONc_scangle_it12.6412
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 197 4.9 %
Rwork0.328 3847 -
obs--89.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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