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- PDB-3l76: Crystal Structure of Aspartate Kinase from Synechocystis -

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Basic information

Entry
Database: PDB / ID: 3l76
TitleCrystal Structure of Aspartate Kinase from Synechocystis
ComponentsAspartokinase
KeywordsTRANSFERASE / Aspartokinase / Synechocystis / Allostery / ACT domains / Kinase
Function / homology
Function and homology information


aspartate kinase / aspartate kinase activity / homoserine biosynthetic process / threonine biosynthetic process / lysine biosynthetic process via diaminopimelate / ATP binding / cytoplasm / 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 / Carbamate kinase / Acetylglutamate kinase-like ...Aspartokinase catalytic domain / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / Aspartokinase signature. / CASTOR, ACT domain / ACT domain / ACT domain / Carbamate kinase / Acetylglutamate kinase-like / ACT domain profile. / ACT domain / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LYSINE / THREONINE / Aspartate kinase
Similarity search - Component
Biological speciesSynechocystis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.54 Å
AuthorsRobin, A. / Cobessi, D. / Curien, G. / Robert-Genthon, M. / Ferrer, J.-L. / Dumas, R.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: A new mode of dimerization of allosteric enzymes with ACT domains revealed by the crystal structure of the aspartate kinase from Cyanobacteria
Authors: Robin, A.Y. / Cobessi, D. / Curien, G. / Robert-Genthon, M. / Ferrer, J.-L. / Dumas, R.
History
DepositionDec 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,35711
Polymers127,1962
Non-polymers1,1619
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-27 kcal/mol
Surface area45580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.210, 237.710, 150.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-605-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 2:43 )
211chain B and (resseq 2:43 )
112chain A and (resseq 77:105 or resseq 113:139 or resseq 144:247 )
212chain B and (resseq 77:105 or resseq 114:140 or resseq 143:247 )
113chain A and (resseq 255:334 )
213chain B and (resseq 255:334 )
114chain A and (resseq 348:418 )
214chain B and (resseq 348:418 )
115chain A and (resseq 432:483 )
215chain B and (resseq 432:483 )
116chain A and (resseq 491:587 )
216chain B and (resseq 491:587 )

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein Aspartokinase / Aspartate kinase


Mass: 63597.871 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis (bacteria) / Strain: PCC 6803 / Gene: lysC, slr0657 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: P74569, aspartate kinase
#2: Chemical
ChemComp-THR / THREONINE


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


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Ammonium sulafte, 0.15 M Ammonium citrate, 9.5% PEG 3350, 2mM lysine, 2mM threonine, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM30A10.97924, 0.97939
SYNCHROTRONESRF ID14-120.934
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 315r1CCDJun 13, 2007Mirrors
ADSC QUANTUM 210r2CCDUndulator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double Si [1 1 1]MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979241
20.979391
30.9341
ReflectionResolution: 2.54→41.4 Å / Num. obs: 51063 / % possible obs: 98 % / Redundancy: 7.33 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 24.9
Reflection shellResolution: 2.54→2.64 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 4.03 / Num. unique all: 5258 / Rsym value: 0.533 / % possible all: 95.3

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Processing

Software
NameVersionClassification
Nemo/Xnemodata collection
SOLVEphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.54→41.4 Å / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.802 / SU ML: 0.4 / σ(F): 1.36 / Phase error: 26.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2547 2553 5 %
Rwork0.1992 --
all0.2021 --
obs0.2021 51050 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.058 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 171.2 Å2 / Biso mean: 61.344 Å2 / Biso min: 5.93 Å2
Baniso -1Baniso -2Baniso -3
1-6.813 Å2-0 Å2-0 Å2
2---1.433 Å20 Å2
3----5.38 Å2
Refinement stepCycle: LAST / Resolution: 2.54→41.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8473 0 77 174 8724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098811
X-RAY DIFFRACTIONf_angle_d1.15212006
X-RAY DIFFRACTIONf_dihedral_angle_d18.2573233
X-RAY DIFFRACTIONf_chiral_restr0.0921496
X-RAY DIFFRACTIONf_plane_restr0.0051576
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A281X-RAY DIFFRACTIONPOSITIONAL
12B281X-RAY DIFFRACTIONPOSITIONAL0.032
21A1069X-RAY DIFFRACTIONPOSITIONAL
22B1069X-RAY DIFFRACTIONPOSITIONAL0.062
31A585X-RAY DIFFRACTIONPOSITIONAL
32B585X-RAY DIFFRACTIONPOSITIONAL0.071
41A484X-RAY DIFFRACTIONPOSITIONAL
42B484X-RAY DIFFRACTIONPOSITIONAL0.068
51A365X-RAY DIFFRACTIONPOSITIONAL
52B365X-RAY DIFFRACTIONPOSITIONAL0.062
61A664X-RAY DIFFRACTIONPOSITIONAL
62B664X-RAY DIFFRACTIONPOSITIONAL0.049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5401-2.63080.34232510.25864758X-RAY DIFFRACTION99
2.6308-2.73610.32912510.25044792X-RAY DIFFRACTION100
2.7361-2.86060.34792540.24034821X-RAY DIFFRACTION100
2.8606-3.01140.30022530.22544818X-RAY DIFFRACTION100
3.0114-3.20.27262550.20224845X-RAY DIFFRACTION100
3.2-3.4470.26852560.20344848X-RAY DIFFRACTION100
3.447-3.79370.22342540.18684828X-RAY DIFFRACTION100
3.7937-4.34210.24752570.1774891X-RAY DIFFRACTION100
4.3421-5.46860.19732590.15124915X-RAY DIFFRACTION100
5.4686-41.43550.21622630.18364981X-RAY DIFFRACTION98
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)
10.1721-0.2007-0.02391.82931.04970.9956-0.00810.055-0.16320.1423-0.28220.29740.438-0.39370.19320.3279-0.17210.00150.1893-0.18080.456625.233973.127447.6568
20.80280.30290.36181.99271.36141.4454-0.0638-0.05470.1323-0.1902-0.19690.2009-0.2109-0.2120.14290.04630.0203-0.0560.027-0.09290.086936.7853105.002860.4624
30.57691.1807-0.43992.7605-0.32774.52180.68630.2267-0.4093-0.08620.51510.30670.14640.0702-1.0550.38970.2492-0.25610.3869-0.0670.49882.2384102.736759.0709
40.0884-0.10280.13291.4636-0.37730.48640.0812-0.06050.27960.684-0.34310.39110.03830.0460.23180.8204-0.27030.14320.0929-0.06440.375738.588741.874559.6975
52.45923.08220.13064.19010.11250.68710.5477-0.20.21611.1276-0.46310.61580.1304-0.0601-0.04370.298-0.0580.2350.0343-0.02990.199826.7647.69652.6251
60.2542-0.40471.22082.9969-1.27096.3425-0.2607-0.2031-0.2629-0.310.5477-0.4721-0.8742-0.4972-0.23611.3151-0.16060.19040.24630.0480.135440.648316.558489.4941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 2:259))A0
2X-RAY DIFFRACTION2chain 'A' and ((resseq 260:589))A0
3X-RAY DIFFRACTION3chain 'A' and ((resseq 590:600))A0
4X-RAY DIFFRACTION4chain 'B' and ((resseq 2:259))B0
5X-RAY DIFFRACTION5chain 'B' and ((resseq 260:589))B0
6X-RAY DIFFRACTION6chain 'B' and ((resseq 590:600))B0

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