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- PDB-3aaw: Crystal structure of aspartate kinase from Corynebacterium glutam... -

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Basic information

Entry
Database: PDB / ID: 3aaw
TitleCrystal structure of aspartate kinase from Corynebacterium glutamicum in complex with lysine and threonine
Components
  • Aspartokinase
  • Aspartokinase LysC beta subunit
KeywordsTRANSFERASE / aspartate kinase / concerted inhibition / Alternative initiation / Amino-acid biosynthesis / ATP-binding / Diaminopimelate biosynthesis / Kinase / Lysine biosynthesis / Nucleotide-binding
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
VC0802-like / Aspartokinase catalytic domain / ACT domain / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / : / ACT domain / Aspartokinase signature. / VC0802-like ...VC0802-like / Aspartokinase catalytic domain / ACT domain / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / : / ACT domain / Aspartokinase signature. / VC0802-like / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LYSINE / THREONINE / Aspartokinase / aspartate kinase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
Corynebacterium crenatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYoshida, A. / Tomita, T. / Kuzuyama, T. / Nishiyama, M.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Mechanism of concerted inhibition of {alpha}2{beta}2-type heterooligomeric aspartate kinase from Corynebacterium glutamicum
Authors: Yoshida, A. / Tomita, T. / Kuzuyama, T. / Nishiyama, M.
#1: 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.
History
DepositionNov 27, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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
A: Aspartokinase
B: Aspartokinase LysC beta subunit
C: Aspartokinase
D: Aspartokinase LysC beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,28511
Polymers128,3674
Non-polymers9187
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15870 Å2
ΔGint-77 kcal/mol
Surface area42020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.232, 162.232, 133.926
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Aspartokinase / Aspartate kinase


Mass: 44798.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: lysC / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL codon plus / References: UniProt: P26512, aspartate kinase
#2: Protein Aspartokinase LysC beta subunit


Mass: 19384.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium crenatum (bacteria) / Gene: lysC / Plasmid: pACYCDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL codon plus / References: UniProt: Q93C54, aspartate kinase
#3: Chemical
ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H9NO3
#4: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H15N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 3.41 Å3/Da / Density % sol: 63.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.2M Sodium citrate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 14, 2007 / Details: mirror
RadiationMonochromator: Triangular Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 59981 / % possible obs: 99.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 59.2 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 27.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 5.8 / Rsym value: 0.338 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2HMF and 2DTJ

2hmf

2dtj


Resolution: 2.5→43.56 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 1 / SU B: 17.94 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25029 3022 5.1 %RANDOM
Rwork0.20985 ---
all0.21188 59980 --
obs0.21188 56782 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 75.7 Å2 / Biso mean: 45.963 Å2 / Biso min: 16.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2---1.36 Å20 Å2
3---2.72 Å2
Refine analyzeLuzzati coordinate error obs: 0.377 Å
Refinement stepCycle: LAST / Resolution: 2.5→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8199 0 62 222 8483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228338
X-RAY DIFFRACTIONr_bond_other_d0.0010.025476
X-RAY DIFFRACTIONr_angle_refined_deg1.0661.97911288
X-RAY DIFFRACTIONr_angle_other_deg0.838313469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.42951090
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57225.143350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.716151472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0841560
X-RAY DIFFRACTIONr_chiral_restr0.0630.21374
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029348
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021512
X-RAY DIFFRACTIONr_mcbond_it0.4931.55474
X-RAY DIFFRACTIONr_mcbond_other0.0581.52246
X-RAY DIFFRACTIONr_mcangle_it0.9428793
X-RAY DIFFRACTIONr_scbond_it1.232864
X-RAY DIFFRACTIONr_scangle_it2.1224.52495
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 240 -
Rwork0.274 4171 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5920.28090.32730.5354-0.05440.29410.02230.08730.0687-0.0793-0.03320.09440.05950.10440.01090.08190.0185-0.01990.10580.02270.0351-29.514425.7765-86.9344
20.56730.14790.11340.82120.16111.34440.03350.10860.151-0.11470.05330.26840.06920.0387-0.08680.10330.0078-0.09520.04310.03740.1716-51.22819.269-95.6471
31.14830.04550.13940.13740.07090.05630.0152-0.04470.18050.0555-0.0133-0.00990.025-0.0223-0.00190.0875-0.00410.01140.095-0.02120.066-1.939.1067-46.5937
41.4086-0.07750.30770.46-0.26671.0563-0.0334-0.22570.57020.0428-0.009-0.10520.0498-0.06950.04240.04770.0147-0.04420.0698-0.11270.28417.040551.6558-37.6423
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 409
2X-RAY DIFFRACTION2B1 - 160
3X-RAY DIFFRACTION3C1 - 409
4X-RAY DIFFRACTION4D1 - 159

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