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

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Basic information

Entry
Database: PDB / ID: 7nsf
TitleTriphosphate tunnel metalloenzyme from Sulfolobus acidocaldarius in complex with triphosphate and magnesium
ComponentsTriphosphate tunnel metalloenzyme Saci_0718
KeywordsHYDROLASE / TTM / CYTH / triphosphate
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
TRIPHOSPHATE / Conserved Archaeal protein
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)23,9813
Polymers23,6991
Non-polymers2822
Water2,018112
1
A: Triphosphate tunnel metalloenzyme Saci_0718
hetero molecules

A: Triphosphate tunnel metalloenzyme Saci_0718
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9626
Polymers47,3982
Non-polymers5654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3060 Å2
ΔGint-50 kcal/mol
Surface area17510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.029, 61.029, 136.619
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

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Components

#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
#2: Chemical ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Reservoir: 0.2 M NaCl, 0.1 M Na/KPO4 pH 6.2, 20% (w/v) PEG 1000 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: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2→43.15 Å / Num. obs: 18208 / % possible obs: 98.93 % / Redundancy: 2 % / Biso Wilson estimate: 43.89 Å2 / CC1/2: 1 / Net I/σ(I): 17.55
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 1778 / CC1/2: 0.967

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Processing

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

7ns9


Resolution: 2→43.15 Å / SU ML: 0.2376 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.7935
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2391 907 5.03 %
Rwork0.2065 17111 -
obs0.2082 18018 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.86 Å2
Refinement stepCycle: LAST / Resolution: 2→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1470 0 14 112 1596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911513
X-RAY DIFFRACTIONf_angle_d1.15972035
X-RAY DIFFRACTIONf_chiral_restr0.0855224
X-RAY DIFFRACTIONf_plane_restr0.0075260
X-RAY DIFFRACTIONf_dihedral_angle_d14.4999594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.130.32431140.27092842X-RAY DIFFRACTION99.97
2.13-2.290.31241480.30032645X-RAY DIFFRACTION93.95
2.29-2.520.29371540.23922819X-RAY DIFFRACTION99.87
2.52-2.880.23511440.23632887X-RAY DIFFRACTION99.93
2.88-3.630.25131760.21772854X-RAY DIFFRACTION99.93
3.63-43.150.2131710.17483064X-RAY DIFFRACTION99.85
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)
12.914771312552.018412770921.069580343052.4417921491-0.4667610645573.657125958940.0264268914292-0.07606379599420.1762961386980.01010615574390.03471495963110.319896794078-0.216951158602-0.0839492511069-9.12366789999E-70.307904695099-0.00263008698089-0.005215869937180.553249666542-0.1693162677820.5637533380245.161348332351.153084896651.3249765093
22.616310311612.329134965670.8550683216992.58806776615-0.4139247347892.953797145060.02466681269190.33724310227-0.271063312852-0.04460986869580.0701454909005-0.6269988925710.4449230314310.3675837025520.00220360864440.3637186836380.0742506995549-0.08973723113230.573552086753-0.145317595810.44953265048241.796447810132.780301598244.2082790997
31.586296625591.275727900841.887281480642.271843901950.9236755171442.517947862290.136955489650.1776507652570.147261021662-0.2131634884910.256880770374-0.206767163311-0.04486421784210.6504285212360.03641394861640.3400618927630.0179800857351-0.003706169510160.540696544083-0.2235578937370.41077999907741.539813763635.730702589739.1782240952
42.430840474970.7883267462611.89105332181.557362497212.208868727773.420661543760.355117821635-0.25409790988-0.08679785362880.434748377225-0.108043915315-0.1015468402550.72006312547-0.05125570371480.000916969739510.413891642620.026443372893-0.0755277433910.429154667363-0.05815119480040.41614205626336.189631331431.604694237145.0842382373
54.954369478450.6065001928511.841496772853.433192573722.631676337953.11929083723-0.05708469556730.6126430611790.104033544599-0.5005407058540.3065278828930.407804716476-0.1498331881420.1586917285840.03255100287390.279299975091-0.00838919195738-0.03576541574380.543594105932-0.1234525294720.32527469628644.644082905646.977757180547.1456561976
60.658540926970.672153526391-0.09242244227820.70160837710.008775474848910.6102944853220.0855679733491.197788243940.800524235784-0.9645214456560.369286843931-0.616780170119-1.206060707890.267022417207-0.005295255853410.563634388884-0.1022837822380.01368571659490.840056617967-0.02242708865890.60724013615353.46583343655.293141736644.5347790023
74.166001000971.34240026520.6973755805820.656763108969-0.4294719675432.00182001450.2233034652230.128328328611-0.9205948439570.1811776213130.0337856502945-0.3255494568530.4101562064220.324960528746-4.8235642199E-60.4117694044450.0659076111513-0.101463932550.602765253432-0.1818123058490.65423879600451.762536208340.584734699853.5842432744
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 2 through 28 )2 - 281 - 27
22chain 'A' and (resid 29 through 53 )29 - 5328 - 52
33chain 'A' and (resid 54 through 89 )54 - 8953 - 88
44chain 'A' and (resid 90 through 117 )90 - 11789 - 116
55chain 'A' and (resid 118 through 142 )118 - 142117 - 141
66chain 'A' and (resid 143 through 156 )143 - 156142 - 155
77chain 'A' and (resid 157 through 178 )157 - 178156 - 177

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