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- PDB-7z66: Crystal structure of the tandem kinase & triphosphate tunnel meta... -

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Basic information

Entry
Database: PDB / ID: 7z66
TitleCrystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with inorganic phosphate and citric acid.
ComponentsInorganic pyrophosphatase TTM1
KeywordsUNKNOWN FUNCTION / triphosphate tunnel metalloenzyme / uridine kinase / cytidine kinase / mitochondrial protein
Function / homology
Function and homology information


regulation of leaf senescence / pyrophosphatase activity / inorganic diphosphatase / inorganic diphosphate phosphatase activity / defense response / kinase activity / mitochondrial outer membrane / ATP binding
Similarity search - Function
CYTH domain / CYTH domain / CYTH domain profile. / CYTH-like domain superfamily / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CITRIC ACID / PHOSPHATE ION / Inorganic pyrophosphatase TTM1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsHothorn, M. / Martinez, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)310856European Union
CitationJournal: To Be Published
Title: Structural and biological insight into the plant unique multimodular triphosphosphate tunnel metalloenzymes of Arabidopsis thaliana
Authors: Pesquera, M. / Martinez, J. / Wang, K. / Hofmann, M. / Loubery, S. / Steensma, P. / Hothorn, M. / Fitzpatrick, T.B.
History
DepositionMar 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAAA: Inorganic pyrophosphatase TTM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9634
Polymers45,6141
Non-polymers3493
Water54030
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.712, 93.712, 267.744
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Inorganic pyrophosphatase TTM1 / Triphosphate tunnel metalloenzyme 1 / AtTTM1


Mass: 45613.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TTM1, At1g73980, F2P9.15 / Plasmid: pMH-HT / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9C9B9, inorganic diphosphatase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.72 Å3/Da / Density % sol: 66.97 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 8,000/20% ethylene glycol, 0.1 M carboxylic acids, 0.1 M Tris, pH 8.5, based on Morpheus condition G10

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99187 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 2.7→46.86 Å / Num. obs: 35969 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 21.2 % / Biso Wilson estimate: 78.54 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.157 / Net I/σ(I): 14.25
Reflection shellResolution: 2.7→2.87 Å / Redundancy: 21.2 % / Num. unique obs: 5749 / CC1/2: 0.584 / Rrim(I) all: 2.512 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→46.86 Å / SU ML: 0.4617 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9095
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2346 1744 4.85 %
Rwork0.213 34198 -
obs0.2142 35942 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.88 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 0 22 30 3216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00163253
X-RAY DIFFRACTIONf_angle_d0.43914404
X-RAY DIFFRACTIONf_chiral_restr0.043490
X-RAY DIFFRACTIONf_plane_restr0.0031571
X-RAY DIFFRACTIONf_dihedral_angle_d11.29341246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.780.42661220.39852809X-RAY DIFFRACTION98.09
2.78-2.870.37221430.33862864X-RAY DIFFRACTION100
2.87-2.970.36881370.30792846X-RAY DIFFRACTION100
2.97-3.090.32751400.30482875X-RAY DIFFRACTION100
3.09-3.230.32481450.31252879X-RAY DIFFRACTION100
3.23-3.410.31881710.25212802X-RAY DIFFRACTION99.9
3.41-3.620.2731540.22622856X-RAY DIFFRACTION99.83
3.62-3.90.23271690.21832815X-RAY DIFFRACTION100
3.9-4.290.24311550.19252864X-RAY DIFFRACTION100
4.29-4.910.19831400.16412852X-RAY DIFFRACTION99.93
4.91-6.180.17931170.19442882X-RAY DIFFRACTION100
6.18-46.860.18091510.17662854X-RAY DIFFRACTION100
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)
11.6725366966-0.935635277989-1.307947932421.766796059711.500142480184.0366473908-0.108391650947-0.0178910740780.1707088791140.2670880469380.1453504510720.152696263555-0.209789995163-0.460362677578-0.04463543146770.8827577966550.1635342547490.1141354761980.544232734740.03230599831030.729744819066-40.673187232822.61018520140.302541323576
24.056104727092.058894179770.8262406116513.476030397820.7473507862722.501377550820.00455126788066-0.2492464080370.0419399583650.173328283422-0.150692217169-0.463403816513-0.4743230025420.6378003805540.1494827079240.856218755702-0.173567588858-0.04477933718120.6270832007350.07632485491030.600723272289-11.220525838617.1875651039-3.74941715186
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: AAAA / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 20 through 238 )20 - 2381 - 219
22chain 'A' and (resid 239 through 412 )239 - 412220 - 393

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