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- PDB-6jbd: Phosphotransferase-ATP complex related to CoA biosynthesis pathway -

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Basic information

Entry
Database: PDB / ID: 6jbd
TitlePhosphotransferase-ATP complex related to CoA biosynthesis pathway
ComponentsPantoate kinase
KeywordsTRANSFERASE / CoA biosynthesis
Function / homology
Function and homology information


pantoate kinase / coenzyme A biosynthetic process / kinase activity / phosphorylation / ATP binding
Similarity search - Function
Pantoate kinase / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / TRIETHYLENE GLYCOL / Pantoate kinase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.5 Å
AuthorsKita, A. / Kishimoto, A. / Shimosaka, T. / Tomita, H. / Yokooji, Y. / Imanaka, T. / Atomi, H. / Miki, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science24.2716 Japan
Japan Society for the Promotion of ScienceJP17J08246 Japan
Japan Society for the Promotion of ScienceJP18H03934 Japan
Other private Japan
CitationJournal: Proteins / Year: 2020
Title: Crystal structure of pantoate kinase from Thermococcus kodakarensis.
Authors: Kita, A. / Kishimoto, A. / Shimosaka, T. / Tomita, H. / Yokooji, Y. / Imanaka, T. / Atomi, H. / Miki, K.
History
DepositionJan 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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_conn.ptnr2_symmetry
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pantoate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,97613
Polymers32,7901
Non-polymers1,18612
Water1,09961
1
A: Pantoate kinase
hetero molecules

A: Pantoate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,95226
Polymers65,5792
Non-polymers2,37224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_466y-1,x+1,-z+11
Buried area5130 Å2
ΔGint-108 kcal/mol
Surface area26020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.323, 95.323, 60.691
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-408-

CA

21A-555-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Pantoate kinase / PoK


Mass: 32789.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK2141 / Production host: Thermococcus kodakarensis (archaea) / References: UniProt: Q5JHF1, pantoate kinase

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Non-polymers , 8 types, 73 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, calcium acetate, ATP, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 11320 / % possible obs: 99.7 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.02 / Rrim(I) all: 0.067 / Χ2: 0.965 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5411.10.3885530.9640.1220.4070.972100
2.54-2.5911.10.3155560.9770.0990.330.961100
2.59-2.6411.20.2965750.9830.0930.3111.001100
2.64-2.6911.10.2565440.9890.0810.2691.163100
2.69-2.7511.20.2315650.990.0720.2430.983100
2.75-2.8211.20.1915440.9910.060.20.944100
2.82-2.8911.10.1765720.9940.0550.1850.945100
2.89-2.9611.20.1535600.9960.0480.1610.952100
2.96-3.0511.10.1245620.9960.0390.130.933100
3.05-3.1511.20.0975640.9970.030.1020.91100
3.15-3.2611.10.085570.9980.0250.0840.904100
3.26-3.3911.10.0695640.9980.0220.0730.923100
3.39-3.55110.0645660.9980.020.0671.033100
3.55-3.73110.0535620.9990.0170.0561.006100
3.73-3.9710.90.0455740.9990.0140.0471.029100
3.97-4.27110.0375680.9990.0120.0390.939100
4.27-4.7110.90.0345730.9990.0110.0360.96100
4.71-5.3910.80.0335830.9990.0110.0350.91100
5.39-6.7910.60.0365850.9990.0110.0380.86100
6.79-1009.30.0335930.9980.0110.0350.96995

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CNS1.3refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
SHARPphasing
RefinementMethod to determine structure: SIR / Resolution: 2.5→100 Å / Cross valid method: THROUGHOUT / σ(F): 235
RfactorNum. reflection% reflection
Rfree0.2594 555 4.9 %
Rwork0.2193 --
obs-11027 97.5 %
Solvent computationBsol: 49.3068 Å2
Displacement parametersBiso max: 85.18 Å2 / Biso mean: 36.8936 Å2 / Biso min: 9.84 Å2
Refinement stepCycle: final / Resolution: 2.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2249 0 60 61 2370
Biso mean--67.14 34.49 -
Num. residues----295
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3331.5
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_mcangle_it2.2372
X-RAY DIFFRACTIONc_scangle_it2.982.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbo2.param
X-RAY DIFFRACTION6CNS_TOPPAR:atp9.param
X-RAY DIFFRACTION7CNS_TOPPAR:p10.par

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