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- PDB-7ns8: Triphosphate tunnel metalloenzyme from Sulfolobus acidocaldarius -

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Basic information

Entry
Database: PDB / ID: 7ns8
TitleTriphosphate tunnel metalloenzyme from Sulfolobus acidocaldarius
ComponentsTriphosphate tunnel metalloenzyme Saci_0718
KeywordsHYDROLASE / TTM / CYTH
Function / homologyAdenylyl cyclase CyaB / CYTH / CYTH domain / CYTH domain / CYTH domain profile. / CYTH-like domain superfamily / ATP binding / metal ion binding / Conserved Archaeal protein
Function and homology information
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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

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Assembly

Deposited unit
A: Triphosphate tunnel metalloenzyme Saci_0718
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1124
Polymers23,6991
Non-polymers4133
Water2,000111
1
A: Triphosphate tunnel metalloenzyme Saci_0718
hetero molecules

A: Triphosphate tunnel metalloenzyme Saci_0718
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2258
Polymers47,3982
Non-polymers8276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3010 Å2
ΔGint-60 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.660, 57.660, 139.150
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-392-

HOH

21A-408-

HOH

31A-411-

HOH

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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-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID / CAPS (buffer)


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Reservoir: 0.2 M Lithium sulfate, 0.1 M CAPS pH 10.5, 2 M Ammonium sulfate 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: ID29 / Wavelength: 0.979003 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979003 Å / Relative weight: 1
ReflectionResolution: 2.3→44.4 Å / Num. obs: 11068 / % possible obs: 99.95 % / Redundancy: 2 % / Biso Wilson estimate: 34.52 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01105 / Rrim(I) all: 0.01563 / Net I/σ(I): 29.77
Reflection shellResolution: 2.3→2.383 Å / Num. unique obs: 1074 / CC1/2: 0.993

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
PHENIX1.19.1_4122refinement
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EEN

2een


Resolution: 2.3→44.4 Å / SU ML: 0.2299 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.867
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2572 535 4.84 %
Rwork0.2259 10530 -
obs0.2273 11065 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.38 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1341 0 24 111 1476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01151381
X-RAY DIFFRACTIONf_angle_d1.15321851
X-RAY DIFFRACTIONf_chiral_restr0.0911205
X-RAY DIFFRACTIONf_plane_restr0.016232
X-RAY DIFFRACTIONf_dihedral_angle_d16.2715534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.530.25721300.22392556X-RAY DIFFRACTION100
2.53-2.90.31041350.26852578X-RAY DIFFRACTION100
2.9-3.650.24591330.22842619X-RAY DIFFRACTION100
3.65-44.40.2461370.21162777X-RAY DIFFRACTION99.86
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)
13.74140591177-0.812066405332-0.4789661681062.03423640312-1.912381670832.255685359810.07276224194020.298663322029-0.555132228749-0.0320358863926-0.04789135431910.02846230585170.517827117365-0.002526819815580.001364720579060.1938842964430.0001272312675870.01393198459660.458879800192-0.03175799713370.2979475631888.57312743737.5369891148248.7316005927
22.758462677831.68603172433-0.1908419325457.37762837138-3.978686138793.264720834620.1823117343890.07858163087110.5693849762740.5324069448050.0334570925460.548388215898-0.427509299772-0.1631767093230.2672002721620.1686073128230.004363754323360.03849561708990.367059064790.1009102033830.283257380193.9065947734418.022178458653.0081572842
31.279689956610.849263526254-0.08069159247432.043767342040.08667796335371.431886493510.298724417629-0.119118701140.05175112802930.251905079083-0.302539932044-0.575549598633-0.01791778718430.247982691970.1229087380560.293107243659-0.0576820354312-0.04632252009380.5509390534210.1369164270380.31598739417112.34362145227.4073168357455.8207446429
41.970010807580.918232060246-0.9072320380742.26045506936-1.159483770152.44386681580.083969541138-0.09621598880740.2123816838150.1369127486290.108532170740.454160217975-0.297497371525-0.2642237607940.06561538854670.182424852520.03195306825540.0183533825880.345163146120.04001622724310.34534576937917.343922859827.551951716342.5481223565
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 118 through 156 )118 - 156104 - 142
22chain 'A' and (resid 157 through 176 )157 - 176143 - 162
33chain 'A' and (resid 6 through 28 )6 - 281 - 23
44chain 'A' and (resid 29 through 117 )29 - 11724 - 103

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