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- PDB-7ns9: Triphosphate tunnel metalloenzyme from Sulfolobus acidocaldarius ... -

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Basic information

Entry
Database: PDB / ID: 7ns9
TitleTriphosphate tunnel metalloenzyme from Sulfolobus acidocaldarius in complex with triphosphate and calcium
ComponentsTriphosphate tunnel metalloenzyme Saci_0718
KeywordsHYDROLASE / TTM / CYTH / triphosphate / calcium
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 / ACETATE ION / DI(HYDROXYETHYL)ETHER / Conserved Archaeal protein
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)24,2026
Polymers23,6991
Non-polymers5035
Water2,468137
1
A: Triphosphate tunnel metalloenzyme Saci_0718
hetero molecules

A: Triphosphate tunnel metalloenzyme Saci_0718
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,40512
Polymers47,3982
Non-polymers1,00710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3950 Å2
ΔGint-81 kcal/mol
Surface area17480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.674, 60.674, 141.086
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 , 5 types, 142 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-3PO / TRIPHOSPHATE


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 59.52 %
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 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: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.75→46 Å / Num. obs: 25885 / % possible obs: 94.31 % / Redundancy: 2 % / Biso Wilson estimate: 32.86 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.44
Reflection shellResolution: 1.75→1.813 Å / Num. unique obs: 2581 / CC1/2: 0.352

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Processing

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

2een


Resolution: 1.75→46 Å / SU ML: 0.2044 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9101
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2354 1340 5.18 %
Rwork0.1886 24541 -
obs0.1909 25881 94.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.48 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 26 137 1628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00771521
X-RAY DIFFRACTIONf_angle_d0.83022043
X-RAY DIFFRACTIONf_chiral_restr0.055226
X-RAY DIFFRACTIONf_plane_restr0.0046258
X-RAY DIFFRACTIONf_dihedral_angle_d14.9999591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.810.34931480.34352433X-RAY DIFFRACTION96.81
1.81-1.890.35741350.29992468X-RAY DIFFRACTION96.59
1.89-1.970.28441190.24752462X-RAY DIFFRACTION96.16
1.97-2.070.24991280.22362449X-RAY DIFFRACTION95.48
2.07-2.20.20651390.19612442X-RAY DIFFRACTION95.35
2.2-2.380.24781450.17882431X-RAY DIFFRACTION95.02
2.38-2.610.23341410.17412453X-RAY DIFFRACTION94.26
2.61-2.990.25621350.20522427X-RAY DIFFRACTION93.23
2.99-3.770.2161270.17962465X-RAY DIFFRACTION92.21
3.77-460.21911230.16692511X-RAY DIFFRACTION88.75
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)
15.222918945871.323452454672.549675373694.101515968260.3509653703246.78374913441-0.122292258705-0.09593304059860.284933977773-0.009021472810810.07087198467980.337030212675-0.200590115595-0.0608757507720.04483576571620.197273987053-0.06979998354590.0240455878680.458637981169-0.1410194935380.51095055723644.714076350950.078851937152.1352562218
22.643773451971.156180894131.910682323712.14849938831.547160499112.926337031210.1033075506990.0692124501691-0.188670863217-0.0580821426710.13314170486-0.2267549677290.187707590950.419287724373-0.1142925492440.2217832342930.0563068817886-0.02859182008060.371722565975-0.08733809211920.34561414712439.581868538835.121365368544.2334009098
37.875694480343.118424535770.8170578995966.022318917350.648442733353.69977090992-0.2298038613420.507285660908-0.295924645657-0.4421106113480.308540227174-0.271842597328-0.0240575714610.193783514688-0.05143229006850.2000392168940.0156363733116-0.005619604526940.480214677871-0.1543712652680.39685021812750.054188036445.691511043851.0473770207
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 1 through 28 )1 - 281 - 28
22chain 'A' and (resid 29 through 127 )29 - 12729 - 127
33chain 'A' and (resid 128 through 178 )128 - 178128 - 178

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