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- PDB-5ysp: Pyrophosphate-dependent kinase in the ribokinase family complexed... -

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Basic information

Entry
Database: PDB / ID: 5ysp
TitlePyrophosphate-dependent kinase in the ribokinase family complexed with a pyrophosphate analog and myo-inositol
ComponentsTM0415
KeywordsTRANSFERASE
Function / homology
Function and homology information


organic substance metabolic process
Similarity search - Function
PPi-dependent kinase / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / METHYLENEDIPHOSPHONIC ACID / Carbohydrate kinase PfkB domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNagata, R. / Fujihashi, M. / Miki, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16J08482 Japan
Japan Society for the Promotion of Science17H05439 Japan
CitationJournal: Nat Commun / Year: 2018
Title: Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants.
Authors: Nagata, R. / Fujihashi, M. / Sato, T. / Atomi, H. / Miki, K.
History
DepositionNov 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TM0415
B: TM0415
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8667
Polymers64,2092
Non-polymers6575
Water1,71195
1
A: TM0415
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4854
Polymers32,1051
Non-polymers3803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TM0415
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3813
Polymers32,1051
Non-polymers2762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.673, 63.009, 89.884
Angle α, β, γ (deg.)90.00, 105.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein TM0415


Mass: 32104.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0415 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9WYP6

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Non-polymers , 5 types, 100 molecules

#2: Chemical ChemComp-INS / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / MYO-INOSITOL / Inositol


Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: neurotransmitter, hormone*YM
#3: Chemical ChemComp-MDN / METHYLENEDIPHOSPHONIC ACID / Medronic acid


Mass: 176.002 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH6O6P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: PEG 4000, ammonium sulfate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 54308 / % possible obs: 98.1 % / Redundancy: 3.3 % / Net I/σ(I): 24.8
Reflection shellResolution: 1.7→1.73 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000715data scaling
MOLREP11.2.08phasing
Coot0.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VK4

1vk4


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.561 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.106 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21042 2727 5 %RANDOM
Rwork0.19644 ---
obs0.19713 51566 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.113 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å20 Å20.61 Å2
2--0.04 Å20 Å2
3---0.59 Å2
Refinement stepCycle: 1 / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4079 0 39 95 4213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194294
X-RAY DIFFRACTIONr_bond_other_d0.0020.023961
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9585839
X-RAY DIFFRACTIONr_angle_other_deg0.91339066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9865565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23822.739157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1515661
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4991528
X-RAY DIFFRACTIONr_chiral_restr0.0780.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024862
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02985
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_it0.4891.4772246
X-RAY DIFFRACTIONr_mcbond_other0.4891.4772245
X-RAY DIFFRACTIONr_mcangle_it0.8122.2112811
X-RAY DIFFRACTIONr_mcangle_other0.8122.2122812
X-RAY DIFFRACTIONr_scbond_it0.5911.5632048
X-RAY DIFFRACTIONr_scbond_other0.5881.5592045
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9412.3153021
X-RAY DIFFRACTIONr_long_range_B_refined2.83612.1024623
X-RAY DIFFRACTIONr_long_range_B_other2.82411.994594
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 185 -
Rwork0.28 3677 -
obs--94.82 %
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)
11.8577-1.0851-0.84976.63361.0952.5366-0.0040.20080.0924-0.235-0.01730.3748-0.3686-0.05980.02120.067-0.0081-0.01960.02410.010.1375-11.85859.448433.3895
22.1852-0.4678-1.11041.28460.9194.5287-0.02340.4111-0.06-0.1214-0.08240.3334-0.0199-0.31930.10580.0487-0.0153-0.00710.0879-0.03530.2161-17.32780.315228.8566
32.48530.75980.18297.51760.32932.1517-0.09070.09920.0743-0.06910.0256-0.0139-0.05690.10590.06510.0276-0.00370.01540.00880.010.1207-10.33373.503740.2331
42.6495-1.0913-1.55215.84490.47644.2922-0.12490.1655-0.375-0.0364-0.01010.14080.37180.00150.1350.0334-0.00020.01450.0146-0.03610.2107-5.4085-9.529634.595
53.3716-0.5177-0.08172.61541.02371.4907-0.0788-0.0327-0.04410.19980.1125-0.20810.00380.1599-0.03380.05430.0121-0.0210.07350.00280.19685.4424-0.132237.497
63.1253-0.05070.62982.58730.29094.1394-0.0190.353-0.154-0.10760.127-0.19250.13620.2789-0.1080.0414-0.00580.05910.2186-0.06890.254310.5481-2.954626.0375
72.5796-1.4946-0.25524.64940.66612.16360.02960.47980.0764-0.4087-0.0548-0.0365-0.22190.26910.02530.1177-0.05860.01040.26510.01430.1421-2.65764.859618.2807
82.53581.06340.39145.41652.28195.1142-0.03510.0556-0.1546-0.228-0.10540.38250.3535-0.25460.14050.20630.01540.01210.13740.01130.211314.562926.3713.8343
94.26851.35181.40581.6224-0.09165.5715-0.03990.06180.2316-0.20910.06250.1187-0.1898-0.6922-0.02260.17250.03130.03060.2074-0.01430.241710.732436.50128.5259
102.29110.12150.19352.66240.38415.03320.01260.10740.0538-0.20780.02450.03120.00460.0634-0.03710.19440.00930.02990.14690.00410.193720.853932.66822.7628
112.1456-0.30350.06224.45551.23235.29760.0007-0.02530.0692-0.00450.0349-0.3060.24870.6393-0.03560.17520.045-0.00570.2791-0.02640.232328.560130.644815.8642
122.1629-1.8833-0.20976.3527-3.04654.58670.0262-0.3371-0.21160.2557-0.039-0.01890.56490.1520.01280.31510.0213-0.04570.2791-0.03220.208822.915925.394626.2896
131.37282.2733-0.26713.8378-0.35865.51720.0915-0.1571-0.09240.1316-0.1885-0.06440.4395-0.58130.0970.2282-0.0168-0.0170.3451-0.02710.217914.270528.028828.582
142.43890.86590.80382.88990.73894.7351-0.0549-0.24490.155-0.00060.09750.13150.2065-0.992-0.04260.1573-0.05720.03150.4046-0.01790.21065.606931.187318.1045
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 23
2X-RAY DIFFRACTION2A24 - 71
3X-RAY DIFFRACTION3A72 - 106
4X-RAY DIFFRACTION4A107 - 138
5X-RAY DIFFRACTION5A139 - 190
6X-RAY DIFFRACTION6A191 - 217
7X-RAY DIFFRACTION7A218 - 280
8X-RAY DIFFRACTION8B1 - 22
9X-RAY DIFFRACTION9B23 - 43
10X-RAY DIFFRACTION10B44 - 121
11X-RAY DIFFRACTION11B122 - 165
12X-RAY DIFFRACTION12B166 - 199
13X-RAY DIFFRACTION13B200 - 218
14X-RAY DIFFRACTION14B219 - 280

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