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- PDB-4go7: The regulatory subunit of aspartate kinase in complex with threon... -

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Basic information

Entry
Database: PDB / ID: 4go7
TitleThe regulatory subunit of aspartate kinase in complex with threonine from Mycobacterium tuberculosis
ComponentsAspartokinase
KeywordsTRANSFERASE
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 / peptidoglycan-based cell wall / phosphorylation / ATP binding / plasma membrane / cytosol
Similarity search - Function
Aspartokinase catalytic domain / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / Aspartokinase signature. / CASTOR, ACT domain / ACT domain / ACT domain / ACT domain / ACT domain profile. ...Aspartokinase catalytic domain / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / Aspartokinase signature. / CASTOR, ACT domain / ACT domain / ACT domain / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
THREONINE / Aspartokinase / Aspartokinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYang, Q. / Li, X.
CitationJournal: Protein Cell / Year: 2011
Title: Structural view of the regulatory subunit of aspartate kinase from Mycobacterium tuberculosis.
Authors: Yang, Q. / Yu, K. / Yan, L. / Li, Y. / Chen, C. / Li, X.
History
DepositionAug 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6212
Polymers21,5021
Non-polymers1191
Water77543
1
X: Aspartokinase
hetero molecules

X: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2434
Polymers43,0042
Non-polymers2382
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y,z1
Buried area4170 Å2
ΔGint-16 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.371, 62.371, 137.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein Aspartokinase / Aspartate kinase / ASK


Mass: 21502.199 Da / Num. of mol.: 1 / Fragment: regulatory subunit (UNP residues 250-421)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ask, Rv3709c, MT3812, MTV025.057c / Production host: Escherichia coli (E. coli)
References: UniProt: P0A4Z8, UniProt: P9WPX3*PLUS, aspartate kinase
#2: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.1 Å3/Da / Density % sol: 60.38 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.8M ammonium phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2011
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 17555
Reflection shellResolution: 2→2.03 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→56.79 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.37 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26425 887 5.1 %RANDOM
Rwork0.21891 ---
obs0.22115 16661 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.059 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2--1.29 Å20 Å2
3----2.58 Å2
Refinement stepCycle: LAST / Resolution: 2→56.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1231 0 8 43 1282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221252
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0741.9691695
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8635161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95624.650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.63415210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.125157
X-RAY DIFFRACTIONr_chiral_restr0.1810.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021912
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_it1.5511.5819
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.54321317
X-RAY DIFFRACTIONr_scbond_it3.3483433
X-RAY DIFFRACTIONr_scangle_it5.3694.5378
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 50 -
Rwork0.299 1204 -
obs--97.89 %

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