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- PDB-7oa2: Triphosphate tunnel metalloenzyme from Sulfolobus acidocaldarius ... -

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Basic information

Entry
Database: PDB / ID: 7oa2
TitleTriphosphate tunnel metalloenzyme from Sulfolobus acidocaldarius in complex with pyrophosphate
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
: / PYROPHOSPHATE 2- / Conserved Archaeal protein
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
DepositionApr 19, 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)23,9143
Polymers23,6991
Non-polymers2152
Water54030
1
A: Triphosphate tunnel metalloenzyme Saci_0718
hetero molecules

A: Triphosphate tunnel metalloenzyme Saci_0718
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8286
Polymers47,3982
Non-polymers4304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3290 Å2
ΔGint-14 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.312, 61.312, 138.535
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(DE3) (bacteria) / Strain (production host): Gold / References: UniProt: Q4JAT2
#2: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Crystals were grown in 1:1 mixtures of JCSG Core IA11 (0.2M Potassium acetate, 20%(w/v) PEG 3350) and 10 mg/ml protein in 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 / 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: 2.7→45.91 Å / Num. obs: 6390 / % possible obs: 78.54 % / Redundancy: 1.9 % / Biso Wilson estimate: 58.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03404 / Rrim(I) all: 0.04814 / Net I/σ(I): 8.7
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 636 / CC1/2: 0.778

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Processing

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

7ns9


Resolution: 2.7→45.91 Å / SU ML: 0.4615 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.1386
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3184 289 4.72 %
Rwork0.2895 5835 -
obs0.291 6124 78.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.29 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1447 0 10 30 1487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01191476
X-RAY DIFFRACTIONf_angle_d1.49971985
X-RAY DIFFRACTIONf_chiral_restr0.1037222
X-RAY DIFFRACTIONf_plane_restr0.0086253
X-RAY DIFFRACTIONf_dihedral_angle_d16.2995566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-3.40.32341430.3362926X-RAY DIFFRACTION80.87
3.4-45.910.31661460.27492909X-RAY DIFFRACTION76.45
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)
13.505436379634.18842817169-0.2230814628631.24781875745-4.387845779283.472002588610.9223245683760.4780058968260.152653458758-1.43310772953-0.796660710081-0.445226659958-0.864503692153-0.27596516591.62967187079E-90.07717908416180.202322569366-0.1541979593080.782503422855-0.2918665352410.51729549080343.378881501242.746650911348.4260302422
23.09016423374-1.429649480152.858184195970.9045866895692.63705426142.957214899840.3499491138030.1906261168970.1294568970170.1185642515160.15530895213-0.1661244420220.2779062103290.485624867882-3.31216979403E-60.4234764960.0766313731131-0.03874436717860.598262122995-0.2345345570070.43226460614339.266050155335.977487693343.1296370918
35.182471252270.03336892375760.9187267003140.7784439159171.023799843322.6912696029-0.3167984892310.637445565979-0.405362426974-0.4346556500960.3396813594590.0425180665248-0.1013485261470.3106354103221.94262460202E-80.458783520127-0.06405274808110.03442562443150.793234867746-0.2577620868690.53952112681650.375324642145.827756532750.326941893
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 53 )2 - 531 - 52
22chain 'A' and (resid 54 through 127 )54 - 12753 - 126
33chain 'A' and (resid 128 through 178 )128 - 178127 - 177

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