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- PDB-3c1m: Cyrstal Structure of threonine-sensitive aspartokinase from Metha... -

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Basic information

Entry
Database: PDB / ID: 3c1m
TitleCyrstal Structure of threonine-sensitive aspartokinase from Methanococcus jannaschii with MgAMP-PNP and L-aspartate
ComponentsProbable aspartokinase
KeywordsTRANSFERASE / kinase / allosteric inhibition / threonine-sensitive / ACT domain / Amino-acid biosynthesis / Threonine biosynthesis
Function / homology
Function and homology information


aspartate kinase / homoserine biosynthetic process / aspartate kinase activity / threonine biosynthetic process / lysine biosynthetic process via diaminopimelate / phosphorylation / ATP binding / cytosol
Similarity search - Function
Lysine-sensitive aspartokinase catalytic domain / VC0802-like / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / Aspartokinase signature. / CASTOR, ACT domain / ACT domain / VC0802-like / ACT domain ...Lysine-sensitive aspartokinase catalytic domain / VC0802-like / Aspartate kinase, monofunctional class / Aspartate kinase / Aspartate kinase, conserved site / Aspartokinase signature. / CASTOR, ACT domain / ACT domain / VC0802-like / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ASPARTIC ACID / FORMIC ACID / Probable aspartokinase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsLiu, X.
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 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: 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_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
C: Probable aspartokinase
D: Probable aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,75922
Polymers205,8294
Non-polymers2,93118
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18570 Å2
MethodPISA
2
A: Probable aspartokinase
B: Probable aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,42612
Polymers102,9142
Non-polymers1,51110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
MethodPISA
3
C: Probable aspartokinase
D: Probable aspartokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,33410
Polymers102,9142
Non-polymers1,4198
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.408, 104.478, 192.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21C
31A
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 3 - 465 / Label seq-ID: 3 - 465

Dom-IDAuth asym-IDLabel asym-ID
1BB
2CC
3AA
4DD

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Probable aspartokinase / Aspartate kinase


Mass: 51457.125 Da / Num. of mol.: 4
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

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Non-polymers , 5 types, 639 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 621 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 14% PEG4000, 100mM Tris, 800mM 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: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 86820 / % possible obs: 78 % / Observed criterion σ(I): 2.9 / Redundancy: 3.5 % / Rsym value: 0.058 / Net I/σ(I): 18.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.305

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementResolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 14.319 / SU ML: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.379 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24613 4369 5 %RANDOM
Rwork0.19375 ---
obs0.19638 82404 95.61 %-
all-86820 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.128 Å2
Baniso -1Baniso -2Baniso -3
1--2.44 Å20 Å20 Å2
2--1.1 Å20 Å2
3---1.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.248 Å0.379 Å
Luzzati d res low-50 Å
Luzzati sigma a-0.3404 Å
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14215 0 182 621 15018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02214563
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.99719627
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.81251860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52724.796565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.451152775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4031589
X-RAY DIFFRACTIONr_chiral_restr0.0950.22341
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210397
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.27234
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.29970
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2851
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0360.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4631.59552
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.759214905
X-RAY DIFFRACTIONr_scbond_it1.28835594
X-RAY DIFFRACTIONr_scangle_it2.1034.54720
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3477 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1BMEDIUM POSITIONAL0.370.5
2CMEDIUM POSITIONAL0.270.5
3AMEDIUM POSITIONAL0.320.5
4DMEDIUM POSITIONAL0.280.5
1BMEDIUM THERMAL0.432
2CMEDIUM THERMAL0.422
3AMEDIUM THERMAL0.442
4DMEDIUM THERMAL0.472
LS refinement shellResolution: 2.3→2.364 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 245 -
Rwork0.253 4880 -
obs--77.36 %
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)
11.34610.4844-0.23110.81710.07391.06030.082-0.1133-0.18270.1635-0.03830.03920.0816-0.0198-0.04370.09220.07210.02180.11440.09180.135531.481919.175967.7345
22.361.72340.86752.83350.99921.38290.1386-0.174-0.21960.279-0.0476-0.05010.219-0.1956-0.0910.0820.05330.04310.18530.0920.128222.93184.855544.491
32.54881.2524-0.13171.54020.85541.61550.0355-0.072-0.38680.05840.1188-0.25950.19610.0018-0.15440.11350.03560.00360.15240.06740.193429.12271.604739.1897
42.9485-0.5769-0.96812.94980.34942.38180.01030.702-0.2904-0.6204-0.08210.1643-0.1137-0.1890.07180.2127-0.0613-0.01570.2733-0.14430.1302-6.1878-11.49144.8521
52.87480.0841-0.25831.08090.1250.8386-0.09120.1414-0.4252-0.0991-0.0245-0.00650.1120.02090.11580.1532-0.0210.09070.1389-0.06460.20922.3087-14.530816.9709
62.02790.0588-0.34472.25731.16942.3314-0.1130.0218-0.0724-0.10950.06760.0287-0.1004-0.12140.04540.05760.01060.00430.16710.06550.122218.13935.894530.0788
72.18920.30850.22761.3312-0.27031.68130.1324-0.2938-0.3570.2059-0.0702-0.15930.1308-0.0223-0.06220.2489-0.02-0.110.19130.13040.2135-0.1952-15.935288.5029
81.65280.15980.06912.3984-1.23672.0830.0046-0.1804-0.03940.0996-0.0025-0.1307-0.0090.0225-0.0020.10650.0223-0.02350.2472-0.04580.1281-16.04370.458971.1401
92.4169-0.1031-0.23981.6963-0.63662.4643-0.0656-0.35780.14030.21320.08640.0819-0.1694-0.0702-0.02080.12690.0089-0.02060.2376-0.0280.1305-22.5335.24174.0846
101.8238-1.6493-0.59563.29280.78441.58230.00570.26140.093-0.1425-0.020.1991-0.16-0.13940.01430.0357-0.05080.00420.0641-0.00990.133-38.584218.855728.1755
110.8563-0.1576-0.04090.61660.15571.2967-0.0501-0.04250.169-0.04010.0894-0.0992-0.12180.0879-0.03930.0818-0.03630.00780.0733-0.03520.2105-30.369721.243640.9796
122.7617-1.0996-0.01011.7359-0.30891.13880.0585-0.0951-0.1731-0.04120.06090.08940.0973-0.06-0.11950.1054-0.0075-0.02970.1838-0.03120.1049-27.2490.542761.0298
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2912 - 291
2X-RAY DIFFRACTION2AA292 - 374292 - 374
3X-RAY DIFFRACTION3AA375 - 470375 - 470
4X-RAY DIFFRACTION4BB2 - 1052 - 105
5X-RAY DIFFRACTION5BB106 - 299106 - 299
6X-RAY DIFFRACTION6BB300 - 470300 - 470
7X-RAY DIFFRACTION7CC2 - 2912 - 291
8X-RAY DIFFRACTION8CC292 - 374292 - 374
9X-RAY DIFFRACTION9CC375 - 470375 - 470
10X-RAY DIFFRACTION10DD2 - 1062 - 106
11X-RAY DIFFRACTION11DD107 - 299107 - 299
12X-RAY DIFFRACTION12DD300 - 470300 - 470

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