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- PDB-5ysq: Sulfate-complex structure of a pyrophosphate-dependent kinase in ... -

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Basic information

Entry
Database: PDB / ID: 5ysq
TitleSulfate-complex structure of a pyrophosphate-dependent kinase in the ribokinase family provides insight into the donor-binding mode
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 / Carbohydrate kinase PfkB domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TM0415
B: TM0415
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9548
Polymers64,2092
Non-polymers7456
Water4,648258
1
A: TM0415
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4774
Polymers32,1051
Non-polymers3723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TM0415
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4774
Polymers32,1051
Non-polymers3723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.745, 62.354, 87.979
Angle α, β, γ (deg.)90.00, 103.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#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 / Comment: neurotransmitter, hormone*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 1.94 Å3/Da / Density % sol: 36.53 %
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: 1.47→50 Å / Num. obs: 79847 / % possible obs: 95.7 % / Redundancy: 3.4 % / Net I/σ(I): 27.8
Reflection shellResolution: 1.47→1.5 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000715data scaling
MOLREP11.2.08phasing
Coot0.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VK4

1vk4


Resolution: 1.47→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.043 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.078 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20448 4017 5 %RANDOM
Rwork0.19243 ---
obs0.19305 75813 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.497 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0 Å2-0.63 Å2
2---0.17 Å20 Å2
3---0.83 Å2
Refinement stepCycle: 1 / Resolution: 1.47→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4269 0 44 258 4571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194660
X-RAY DIFFRACTIONr_bond_other_d0.0020.024290
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.9616352
X-RAY DIFFRACTIONr_angle_other_deg0.99339898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4145613
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.92122.834187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86715764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7641536
X-RAY DIFFRACTIONr_chiral_restr0.1020.2728
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025297
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021028
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_it0.3990.7432374
X-RAY DIFFRACTIONr_mcbond_other0.3990.7432373
X-RAY DIFFRACTIONr_mcangle_it0.6711.1123004
X-RAY DIFFRACTIONr_mcangle_other0.6711.1133005
X-RAY DIFFRACTIONr_scbond_it0.5570.8062286
X-RAY DIFFRACTIONr_scbond_other0.5560.8042271
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8541.1843322
X-RAY DIFFRACTIONr_long_range_B_refined2.5319.1335117
X-RAY DIFFRACTIONr_long_range_B_other2.4998.9735083
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 254 -
Rwork0.248 5466 -
obs--92.77 %
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)
11.1365-0.3260.65361.4748-0.65952.98970.00820.1174-0.0047-0.1122-0.0574-0.36170.12390.15850.04920.01210.00630.03180.01640.01040.144716.1787-4.424530.4359
21.99671.10890.06636.782-0.82222.3683-0.09450.1113-0.0777-0.06140.0828-0.17870.0185-0.1260.01170.01450.0109-0.00910.0442-0.02890.06611.1388-1.003138.6569
30.8748-0.20170.25451.51190.16541.0493-0.0137-0.020.031-0.0968-0.06020.0812-0.0205-0.16120.07390.0150.01150.01530.0557-0.01070.0799-0.61070.080127.0757
41.2181-0.20030.25881.7848-0.2661.5223-0.02180.05160.0179-0.14870.0159-0.1548-0.05020.05410.00590.09380.01650.01990.0931-0.03910.0758-14.7499-29.05092.7638
50.9185-0.36630.10171.52860.10371.4374-0.0291-0.0882-0.05170.13410.04980.1334-0.0027-0.107-0.02070.08230.02650.02830.0874-0.00910.0958-24.8961-27.990615.9042
65.9992.01540.13294.8830.05283.00050.075-0.33650.01980.2486-0.11820.27060.0272-0.16780.04310.13050.0371-0.00450.128-0.00050.07-17.4575-27.753926.4845
71.42950.6298-0.65931.4808-0.0031.2454-0.0448-0.1122-0.11980.13140.0397-0.0167-0.09260.0350.00510.10240.0199-0.03220.10860.00190.1025-7.841-31.112521.868
84.2095-2.41490.09946.0696-0.3443.56120.14590.085-0.3274-0.0941-0.1171-0.5550.12150.5914-0.02870.1398-0.02250.00220.1379-0.02430.18060.0414-29.77939.8226
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 78
2X-RAY DIFFRACTION2A79 - 108
3X-RAY DIFFRACTION3A109 - 285
4X-RAY DIFFRACTION3A301
5X-RAY DIFFRACTION3A302
6X-RAY DIFFRACTION3A303
7X-RAY DIFFRACTION4B1 - 88
8X-RAY DIFFRACTION5B89 - 192
9X-RAY DIFFRACTION5B301
10X-RAY DIFFRACTION5B302
11X-RAY DIFFRACTION5B303
12X-RAY DIFFRACTION6B193 - 209
13X-RAY DIFFRACTION7B210 - 264
14X-RAY DIFFRACTION8B265 - 280

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