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- PDB-3ab2: Crystal structure of aspartate kinase from Corynebacterium glutam... -

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Basic information

Entry
Database: PDB / ID: 3ab2
TitleCrystal structure of aspartate kinase from Corynebacterium glutamicum in complex with threonine
Components(AspartokinaseAspartate kinase) x 2
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 / threonine biosynthetic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / phosphorylation / ATP binding
Similarity search - Function
VC0802-like / Aspartokinase catalytic domain / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / Aspartokinase signature. / CASTOR, ACT domain / ACT domain / VC0802-like / ACT domain ...VC0802-like / Aspartokinase catalytic domain / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / Aspartokinase signature. / CASTOR, ACT domain / ACT domain / VC0802-like / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THREONINE / Aspartokinase
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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 30, 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
C: Aspartokinase
D: Aspartokinase
E: Aspartokinase
F: Aspartokinase
G: Aspartokinase
H: Aspartokinase
I: Aspartokinase
J: Aspartokinase
K: Aspartokinase
L: Aspartokinase
M: Aspartokinase
N: Aspartokinase
O: Aspartokinase
P: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)515,25331
Polymers513,46616
Non-polymers1,78715
Water4,432246
1
A: Aspartokinase
B: Aspartokinase
C: Aspartokinase
D: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,8438
Polymers128,3674
Non-polymers4764
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12470 Å2
ΔGint-73 kcal/mol
Surface area41240 Å2
MethodPISA
2
E: Aspartokinase
F: Aspartokinase
G: Aspartokinase
H: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,8438
Polymers128,3674
Non-polymers4764
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12260 Å2
ΔGint-72 kcal/mol
Surface area41190 Å2
MethodPISA
3
I: Aspartokinase
J: Aspartokinase
K: Aspartokinase
L: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,7247
Polymers128,3674
Non-polymers3573
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12250 Å2
ΔGint-76 kcal/mol
Surface area41090 Å2
MethodPISA
4
M: Aspartokinase
N: Aspartokinase
O: Aspartokinase
P: Aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,8438
Polymers128,3674
Non-polymers4764
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12880 Å2
ΔGint-71 kcal/mol
Surface area41470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.833, 119.093, 124.384
Angle α, β, γ (deg.)71.85, 69.48, 72.72
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Aspartokinase / Aspartate kinase / Aspartate kinase


Mass: 44798.527 Da / Num. of mol.: 8
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 / Aspartate kinase / Aspartate kinase


Mass: 19384.752 Da / Num. of mol.: 8 / Fragment: ACT 1/2 domains, UNP residues 251-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: lysC / Plasmid: pACYCDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL codon plus / References: UniProt: P26512, aspartate kinase
#3: Chemical
ChemComp-THR / THREONINE / Threonine


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C4H9NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.2M Ammonium sulfate, 0.05M HEPES-NaOH, 2.1% PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 156726 / % possible obs: 98.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 79.2 Å2 / Rmerge(I) obs: 0.15 / Rsym value: 0.15 / Net I/σ(I): 6.7
Reflection shellResolution: 2.59→2.69 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 0.84 / Rsym value: 0.47 / % possible all: 96.4

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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 ENTRY 3AAW

3aaw


Resolution: 2.59→42.04 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.904 / SU B: 30.733 / SU ML: 0.291 / Cross valid method: THROUGHOUT / ESU R: 0.817 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28025 7700 5 %RANDOM
Rwork0.23198 ---
obs0.2344 146136 97.13 %-
all-153824 --
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 mean: 62.201 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20.01 Å2-0.01 Å2
2--0 Å2-0.01 Å2
3---0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.411 Å
Refinement stepCycle: LAST / Resolution: 2.59→42.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31609 0 120 246 31975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02232005
X-RAY DIFFRACTIONr_bond_other_d0.0010.0220728
X-RAY DIFFRACTIONr_angle_refined_deg0.9051.97343386
X-RAY DIFFRACTIONr_angle_other_deg0.787351004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.34454257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15825.1931292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.786155437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.39915213
X-RAY DIFFRACTIONr_chiral_restr0.0510.25335
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0236016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025817
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_it0.2341.521333
X-RAY DIFFRACTIONr_mcbond_other0.0241.58780
X-RAY DIFFRACTIONr_mcangle_it0.437234103
X-RAY DIFFRACTIONr_scbond_it0.498310672
X-RAY DIFFRACTIONr_scangle_it0.8944.59283
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.589→2.656 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 489 -
Rwork0.381 9049 -
obs--81.89 %
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)
10.97280.03020.77890.44140.64641.93650.11870.0582-0.1142-0.026-0.0122-0.07710.1450.0496-0.10650.09730.01640.07050.00570.00360.1036-1.1174-0.04540.5917
22.58150.03670.11920.76820.22622.27550.1673-0.2525-0.34360.0037-0.0083-0.18550.35380.1048-0.1590.06520.0012-0.03940.03560.04240.12610.5027-4.871821.8384
30.6851-0.13910.43671.1266-1.06111.9995-0.0403-0.07-0.0138-0.29230.24970.13810.2503-0.1797-0.20940.1746-0.061-0.00750.06910.00560.0788-47.00187.0322-24.5732
42.5640.1244-0.50972.3520.46381.5185-0.1620.208-0.3064-0.55010.34450.3160.4743-0.487-0.18250.5693-0.3142-0.22070.26590.14210.1878-61.32366.2798-45.1634
50.5052-0.61750.08572.2105-0.61770.3794-0.03040.08330.13170.00270.0221-0.18010.0086-0.10240.00830.09010.00440.04340.1271-0.03340.1273-6.259320.4381-50.5934
63.2075-0.31610.36931.7379-0.3141.8755-0.07640.3827-0.199-0.1980.1464-0.26820.2195-0.1267-0.070.1659-0.04540.09060.1213-0.0770.11760.5781-3.3643-54.6194
70.575-0.08390.23612.63990.34260.974-0.0646-0.0495-0.0888-0.03780.08230.09040.0504-0.0468-0.01780.0782-0.00450.04770.03810.03360.0647-42.989557.6151-43.692
81.6949-0.3642-0.1361.80770.32183.0276-0.1094-0.020.0677-0.12880.02510.18-0.3016-0.22090.08430.16030.03360.01530.01910.00190.0416-49.702381.4495-44.7379
90.8457-0.12150.30760.63910.72022.5609-0.195-0.0290.2287-0.06480.0244-0.1078-0.28880.34950.17060.0687-0.0231-0.05170.08370.06020.2453.698369.5736-31.507
102.0678-0.5059-0.57412.6764-0.21172.2514-0.24350.2010.5035-0.29250.2305-0.1076-0.45960.67780.0130.2446-0.2744-0.07290.34790.14480.34610.419271.8611-55.1012
110.1985-0.12-0.08140.8746-0.48192.2762-0.02230.0120.03490.095-0.09020.1108-0.2688-0.1770.11240.0660.0412-0.02560.0778-0.06480.0732-32.093474.95617.0438
122.5578-0.0253-0.16852.3754-0.19831.7307-0.1856-0.07270.23890.5285-0.02320.1618-0.5696-0.32610.20880.38290.06670.00520.1177-0.09840.119-38.270679.126930.4824
130.50620.4630.02421.9376-0.8810.791-0.1001-0.04680.00190.1313-0.0576-0.2553-0.07150.03520.15770.06820.01-0.02510.1678-0.1330.17559.199449.772419.7687
142.7288-0.02040.0632.07470.2521.5453-0.1121-0.14790.18880.3427-0.0936-0.2689-0.36560.14810.20570.1945-0.0163-0.18390.1301-0.07540.272722.293471.059120.0384
150.72020.71510.0942.09070.48150.36310.0676-0.05870.0590.1199-0.0120.0589-0.03120.018-0.05550.11350.03130.06150.07720.01330.0399-35.797124.412826.0841
161.792-0.33890.62451.8197-0.04441.63030.0861-0.0758-0.17510.2684-0.09250.15270.0224-0.12460.00630.1215-0.01540.04520.04720.01530.0547-47.12973.25530.1372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 409
2X-RAY DIFFRACTION2B1 - 160
3X-RAY DIFFRACTION3C2 - 408
4X-RAY DIFFRACTION4D4 - 158
5X-RAY DIFFRACTION5E2 - 408
6X-RAY DIFFRACTION6F3 - 158
7X-RAY DIFFRACTION7G1 - 408
8X-RAY DIFFRACTION8H2 - 158
9X-RAY DIFFRACTION9I2 - 409
10X-RAY DIFFRACTION10J3 - 156
11X-RAY DIFFRACTION11K2 - 409
12X-RAY DIFFRACTION12L4 - 158
13X-RAY DIFFRACTION13M2 - 408
14X-RAY DIFFRACTION14N3 - 157
15X-RAY DIFFRACTION15O2 - 411
16X-RAY DIFFRACTION16P1 - 159

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