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- PDB-7z67: Crystal structure of the tandem kinase & triphosphate tunnel meta... -

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Basic information

Entry
Database: PDB / ID: 7z67
TitleCrystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with a adenosine nucleotide analog.
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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / CITRIC ACID / Inorganic pyrophosphatase TTM1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 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 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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
A: Inorganic pyrophosphatase TTM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4216
Polymers45,6141
Non-polymers8075
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-15 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.370, 93.370, 266.327
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

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 9 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#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-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.68 Å3/Da / Density % sol: 66.55 %
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, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 2.65→46.69 Å / Num. obs: 37785 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 19.2 % / Biso Wilson estimate: 77.75 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.164 / Net I/σ(I): 13
Reflection shellResolution: 2.65→2.8 Å / Redundancy: 19 % / Num. unique obs: 6002 / CC1/2: 0.516 / Rrim(I) all: 2.796 / % possible all: 97.9

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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: 2.65→46.69 Å / SU ML: 0.4017 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.9753
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2445 1817 4.82 %
Rwork0.2188 35914 -
obs0.2202 37731 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.91 Å2
Refinement stepCycle: LAST / Resolution: 2.65→46.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 0 50 4 3218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00193288
X-RAY DIFFRACTIONf_angle_d0.50664459
X-RAY DIFFRACTIONf_chiral_restr0.043495
X-RAY DIFFRACTIONf_plane_restr0.0036573
X-RAY DIFFRACTIONf_dihedral_angle_d12.90141255
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.720.41321160.40082659X-RAY DIFFRACTION95.76
2.72-2.80.38171270.34142783X-RAY DIFFRACTION100
2.8-2.890.32331410.30672773X-RAY DIFFRACTION99.97
2.89-2.990.31391360.30042772X-RAY DIFFRACTION99.97
2.99-3.110.28251370.29662808X-RAY DIFFRACTION100
3.11-3.250.32581320.30042763X-RAY DIFFRACTION100
3.25-3.420.30181690.23782751X-RAY DIFFRACTION99.79
3.42-3.640.29091500.24012731X-RAY DIFFRACTION99.93
3.64-3.920.25141620.22292780X-RAY DIFFRACTION100
3.92-4.310.25941470.20092737X-RAY DIFFRACTION100
4.31-4.940.20011440.17152788X-RAY DIFFRACTION100
4.94-6.220.20071080.20612809X-RAY DIFFRACTION100
6.22-46.690.19911480.18042760X-RAY DIFFRACTION99.97
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)
12.31982474226-1.21637964179-1.682524550532.654563078951.502230255574.39778738151-0.163745285305-0.1556165777240.2811449853450.4159226166610.1960498837490.286364678053-0.285234238493-0.53694919041-0.004022285868530.8756393046420.1829914112810.09922528356450.5291956546770.02145931249190.663829445529-40.632627693822.61857008090.256093732539
25.1545472592.618963458890.8145392829323.740789789840.8333780999532.832438935750.0500186759083-0.2652312870890.009619713845980.140170001922-0.192549938412-0.531945969919-0.4625539885730.7515328820740.1314247410880.835396766427-0.160014277922-0.04473565633970.5972741768570.07952797775150.560037394159-11.235655512917.1920400338-3.72098672579
Refinement TLS group

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