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- PDB-3c20: Crystal Structure of Threonine-sensitive Aspartokinase from Metha... -

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Basic information

Entry
Database: PDB / ID: 3c20
TitleCrystal Structure of Threonine-sensitive Aspartokinase from Methanococcus jannaschii with L-aspartate
ComponentsProbable aspartokinase
KeywordsTRANSFERASE / kinase / allosetric inhibition / theronine-sensitive / ACT domain / Amino-acid biosynthesis / Threonine biosynthesis
Function / homology
Function and homology information


aspartate kinase / aspartate kinase activity / homoserine biosynthetic process / threonine biosynthetic process / lysine biosynthetic process via diaminopimelate / ATP binding / cytosol
Similarity search - Function
Lysine-sensitive aspartokinase catalytic domain / VC0802-like / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / : / ACT domain / Aspartokinase signature. / VC0802-like / ACT domain ...Lysine-sensitive aspartokinase catalytic domain / VC0802-like / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / : / ACT domain / Aspartokinase signature. / VC0802-like / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ASPARTIC ACID / FORMIC ACID / Probable aspartokinase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsLiu, X. / Pavlovsky, A.G. / Viola, R.E.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The Structural Basis for Allosteric Inhibition of a Threonine-sensitive Aspartokinase.
Authors: Liu, X. / Pavlovsky, A.G. / Viola, R.E.
History
DepositionJan 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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

Downloads & links

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Assembly

Deposited unit
A: Probable aspartokinase
B: Probable aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2736
Polymers102,9142
Non-polymers3584
Water23413
1
A: Probable aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6363
Polymers51,4571
Non-polymers1792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6363
Polymers51,4571
Non-polymers1792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.973, 199.071, 96.394
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12B
22A
13B
23A
14A
24B
15A
25B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRGLNGLN1AA2 - 552 - 55
21THRTHRGLNGLN1BB2 - 552 - 55
12ALAALAGLUGLU2BB56 - 13056 - 130
22ALAALAGLUGLU2AA56 - 13056 - 130
13ARGARGLEULEU1BB131 - 260131 - 260
23ARGARGLEULEU1AA131 - 260131 - 260
14ALAALACYSCYS2AA261 - 405261 - 405
24ALAALACYSCYS2BB261 - 405261 - 405
15VALVALLYSLYS1AA406 - 470406 - 470
25VALVALLYSLYS1BB406 - 470406 - 470

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein Probable aspartokinase / Aspartate kinase


Mass: 51457.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0571 / Plasmid: pET41a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q57991, aspartate kinase
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14% PEG4000, 0.1M Tris, 0.8M ammonium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.039 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.039 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 30974 / % possible obs: 0.91 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rsym value: 0.076 / Net I/σ(I): 28.3
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3 / Rsym value: 0.395

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementStarting model: PDB code:3C1M

3c1m


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.903 / SU B: 37.776 / SU ML: 0.353 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27298 1466 5.1 %RANDOM
Rwork0.23794 ---
obs0.23976 27389 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.893 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2---1.95 Å20 Å2
3---0.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.383 Å-
Luzzati sigma a-0.4543 Å
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7075 0 24 13 7112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227178
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1831.9879666
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7115927
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.12224.892278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.517151369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4111542
X-RAY DIFFRACTIONr_chiral_restr0.110.21161
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025156
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.23712
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.25016
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2256
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3711.54732
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.65327440
X-RAY DIFFRACTIONr_scbond_it0.79832677
X-RAY DIFFRACTIONr_scangle_it1.4284.52226
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A406tight positional0.020.05
2B300tight positional0.030.05
3B983tight positional0.030.05
4A556tight positional0.060.05
5A475tight positional0.030.05
2B311medium positional0.60.5
4A491medium positional0.830.5
1A406tight thermal0.040.5
2B300tight thermal0.040.5
3B983tight thermal0.050.5
4A556tight thermal0.040.5
5A475tight thermal0.050.5
2B311medium thermal0.292
4A491medium thermal0.282
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 120 -
Rwork0.294 1967 -
obs--99.52 %
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)
11.7688-0.027-1.47992.31690.10133.9834-0.0925-0.1558-0.34320.0033-0.045-0.1846-0.05240.4360.13740.2339-0.11160.01880.2023-0.08340.1208-25.121-7.663-27.335
23.81261.9613-2.26599.59323.61434.00830.3137-0.07020.28490.2809-0.28910.3151-0.2503-0.1914-0.02460.36450.02330.03830.1918-0.10460.172-38.8267.057-22.663
35.17233.32120.78465.73630.78571.6418-0.05130.1391-1.0913-0.20980.3197-1.24360.02430.1682-0.26840.2105-0.01670.19690.0631-0.17320.3912-26.22720.145-4.665
42.78070.6177-0.9011.8997-0.82781.27190.13950.11890.01830.4892-0.06070.0094-0.1604-0.0316-0.07880.1234-0.0210.0450.099-0.05770.0946-10.46558.708-0.735
58.14262.5273-1.1348.4231-0.39440.15820.2436-0.2467-0.31040.3831-0.27160.46950.1618-0.33160.0280.1934-0.1450.09970.2037-0.01840.1596-21.98644.6537.852
63.5749-0.0841-1.96044.10290.8223.6614-0.21930.5327-0.2268-0.79830.1826-0.4119-0.0253-0.2080.03680.2661-0.1110.17170.1467-0.11320.1472-30.53531.746-12.715
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2582 - 258
2X-RAY DIFFRACTION2AA259 - 309259 - 309
3X-RAY DIFFRACTION3AA310 - 470310 - 470
4X-RAY DIFFRACTION4BB2 - 2582 - 258
5X-RAY DIFFRACTION5BB259 - 309259 - 309
6X-RAY DIFFRACTION6BB310 - 470310 - 470

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