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- PDB-2j0w: Crystal structure of E. coli aspartokinase III in complex with as... -

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Basic information

Entry
Database: PDB / ID: 2j0w
TitleCrystal structure of E. coli aspartokinase III in complex with aspartate and ADP (R-state)
ComponentsLYSINE-SENSITIVE ASPARTOKINASE 3
KeywordsTRANSFERASE / FEEDBACK INHIBITION / ALLOSTERIC REGULATION / KINASE / ACT DOMAIN / ASPARTOKINASE / AMINO ACID BIOSYNTHESIS / AMINO-ACID BIOSYNTHESIS / ASPARTATE PATHWAY / LYSINE BIOSYNTHESIS
Function / homology
Function and homology information


aspartate kinase / homoserine biosynthetic process / aspartate kinase activity / lysine biosynthetic process via diaminopimelate / phosphorylation / 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 / Aspartokinase signature. / ACT domain / ACT domain ...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 / Aspartokinase signature. / ACT domain / ACT domain / Carbamate kinase / Acetylglutamate kinase-like / ACT domain profile. / ACT domain / ACT-like domain / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 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
ADENOSINE-5'-DIPHOSPHATE / ASPARTIC ACID / Lysine-sensitive aspartokinase 3
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.3Dec 13, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSINE-SENSITIVE ASPARTOKINASE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2005
Polymers48,5791
Non-polymers6204
Water1,22568
1
A: LYSINE-SENSITIVE ASPARTOKINASE 3
hetero molecules

A: LYSINE-SENSITIVE ASPARTOKINASE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,39910
Polymers97,1592
Non-polymers1,2408
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_558x,-y,-z+31
MethodPQS
Unit cell
Length a, b, c (Å)49.535, 213.347, 93.078
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 48579.469 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 72 molecules

#2: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartic acid


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.53 Å3/Da / Density % sol: 51.48 %
Crystal growpH: 8.4
Details: 0.2M AMMONIUM NITRATE, 0.1M TRIS, PH 8.4, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 17477 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 37.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J0X

2j0x


Resolution: 2.5→29.79 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2322172.79 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.293 884 5.1 %RANDOM
Rwork0.235 ---
obs0.235 17467 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.6069 Å2 / ksol: 0.262627 e/Å3
Displacement parametersBiso mean: 64.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.83 Å20 Å20 Å2
2---13.11 Å20 Å2
3---16.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3395 0 38 68 3501
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.482
X-RAY DIFFRACTIONc_mcangle_it4.094
X-RAY DIFFRACTIONc_scbond_it6.084
X-RAY DIFFRACTIONc_scangle_it8.518
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.424 156 5.5 %
Rwork0.359 2704 -
obs--99.8 %
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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