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- PDB-7nsa: Triphosphate tunnel metalloenzyme from Sulfolobus acidocaldarius ... -

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Basic information

Entry
Database: PDB / ID: 7nsa
TitleTriphosphate tunnel metalloenzyme from Sulfolobus acidocaldarius in complex with pyrophosphate and calcium
ComponentsTriphosphate tunnel metalloenzyme Saci_0718
KeywordsHYDROLASE / TTM / CYTH / pyrophosphate
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
Adenylyl cyclase CyaB / CYTH / CYTH domain / CYTH domain / CYTH domain profile. / CYTH-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / PYROPHOSPHATE 2- / Conserved Archaeal protein
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsVogt, M.S. / Essen, L.-O. / Banerjee, A.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB987 Germany
Volkswagen FoundationAz96727 Germany
German Research Foundation (DFG)707228-809188 Germany
Citation
Journal: J.Biol.Chem. / Year: 2021
Title: The archaeal triphosphate tunnel metalloenzyme SaTTM defines structural determinants for the diverse activities in the CYTH protein family.
Authors: Vogt, M.S. / Ngouoko Nguepbeu, R.R. / Mohr, M.K.F. / Albers, S.V. / Essen, L.O. / Banerjee, A.
#1: Journal: Biorxiv / Year: 2021
Title: The archaeal triphosphate tunnel metalloenzyme Sa TTM defines structural determinants for the diverse activities in the CYTH protein family
Authors: Vogt, M.S. / Nguepbeu, R.R.N. / Mohr, M.K.F. / Albers, S.V. / Essen, L.O. / Banerjee, A.
History
DepositionMar 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _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: Triphosphate tunnel metalloenzyme Saci_0718
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1726
Polymers23,6991
Non-polymers4735
Water2,252125
1
A: Triphosphate tunnel metalloenzyme Saci_0718
hetero molecules

A: Triphosphate tunnel metalloenzyme Saci_0718
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,34512
Polymers47,3982
Non-polymers94710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3940 Å2
ΔGint-43 kcal/mol
Surface area17270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.545, 60.545, 141.627
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-201-

ACT

21A-201-

ACT

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Triphosphate tunnel metalloenzyme Saci_0718 / Conserved Archaeal protein / Adenylate cyclase


Mass: 23698.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770) (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Gene: Saci_0718
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q4JAT2

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Non-polymers , 6 types, 130 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.74 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Reservoir: 0.17 M Ammonium acetate, 0.085 M Sodium acetate pH 4.6, 25.5% (w/v) PEG 4000, 15% (v/v) glycerol Protein buffer: 200 mM NaCl, 50 mM Tris, pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.95→46.02 Å / Num. obs: 19769 / % possible obs: 98.87 % / Redundancy: 2 % / Biso Wilson estimate: 37.37 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.6
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 1955 / CC1/2: 0.729

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.19.1_4122refinement
Aimlessdata scaling
SCALAdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NS9

7ns9


Resolution: 1.95→46.02 Å / SU ML: 0.2067 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.1382
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2458 1017 5.14 %
Rwork0.225 18751 -
obs0.226 19768 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.2 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 27 125 1614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01771510
X-RAY DIFFRACTIONf_angle_d1.92232024
X-RAY DIFFRACTIONf_chiral_restr0.1127223
X-RAY DIFFRACTIONf_plane_restr0.0104256
X-RAY DIFFRACTIONf_dihedral_angle_d18.1094589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.050.28941300.30322633X-RAY DIFFRACTION99.25
2.05-2.180.2661490.27172617X-RAY DIFFRACTION99.18
2.18-2.350.29081570.25142608X-RAY DIFFRACTION99.18
2.35-2.590.25171560.23852648X-RAY DIFFRACTION99.05
2.59-2.960.26371430.24362673X-RAY DIFFRACTION98.67
2.96-3.730.22351440.2152699X-RAY DIFFRACTION98.78
3.73-46.020.23591380.2052873X-RAY DIFFRACTION98.11
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)
15.61654845071.975701648340.9878253647343.366007603732.269873928393.31099128977-0.04234789687770.358098081006-0.0268010776634-0.2153059766320.0669177646809-0.206378973739-0.1719537791390.20136447868-7.08380944793E-50.2087495591310.0246401233695-0.002565459340310.447688606994-0.1281895861220.30168930341849.876628118646.12441966950.711551666
22.967391277191.433053263630.3485212180732.09362511337-0.7551892387851.62463887266-0.117894214161-0.0215766592940.433651136401-0.1633956864580.08828642406670.247438838615-0.25327440605-0.173521708901-0.001144575475690.326301736643-0.00419746546660.01129114448640.511575789802-0.1250805757930.43980284778744.564114656850.639057410152.5007237865
32.496757263551.715662197211.058203254181.35965906240.1439226859742.29646620590.09371492223160.00609992590221-0.123049432781-0.06014992475630.137506273199-0.2321748440950.1571729166010.3032038803320.1066287118360.2292385222920.0639425969326-0.06265009956130.377171814895-0.1317377982170.30569363529339.051342901933.319755918844.5644189806
40.6728202247420.2217619673660.6774993999180.8724181323690.6406964673380.9614987679840.2541970099720.1054598823690.0324933525875-0.2679381348750.048102473855-0.221427038577-0.1649459851620.7192990435150.002006788942880.4265380525330.0323678250199-0.02517578043420.597320863364-0.1597525215520.40674468880245.389930380836.876013567938.9981684154
52.843365833011.495972451291.658524708361.723376305732.058571487873.190190661790.209464896583-0.2137512640890.08958588523880.325209991065-0.1062610524970.2251231829110.4833013420760.08940329360360.02357082637630.2129215823130.0579093853741-0.04915154190760.336054311319-0.05163448981550.25407272711137.295717844635.567514663447.0604291552
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 128 through 176 )128 - 176127 - 175
22chain 'A' and (resid 2 through 28 )2 - 281 - 27
33chain 'A' and (resid 29 through 69 )29 - 6928 - 68
44chain 'A' and (resid 70 through 89 )70 - 8969 - 88
55chain 'A' and (resid 90 through 127 )90 - 12789 - 126

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