[English] 日本語
Yorodumi
- PDB-7nsd: Triphosphate tunnel metalloenzyme from Sulfolobus acidocaldarius ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7nsd
TitleTriphosphate tunnel metalloenzyme from Sulfolobus acidocaldarius in complex with ATP and calcium
ComponentsTriphosphate tunnel metalloenzyme Saci_0718
KeywordsHYDROLASE / TTM / CYTH / ATP
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 / ADENOSINE-5'-TRIPHOSPHATE / Conserved Archaeal protein
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Triphosphate tunnel metalloenzyme Saci_0718
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3455
Polymers23,6991
Non-polymers6464
Water1,38777
1
A: Triphosphate tunnel metalloenzyme Saci_0718
hetero molecules

A: Triphosphate tunnel metalloenzyme Saci_0718
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,69110
Polymers47,3982
Non-polymers1,2938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4770 Å2
ΔGint-70 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.670, 60.670, 139.350
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

-
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-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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Reservoir: 0.2 M Calcium acetate, 0.1 M MES pH 6.0, 20% (w/v) PEG 8000 Protein buffer: 200 mM NaCl, 50 mM Tris, pH 9.0

-
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: 2.19→45.75 Å / Num. obs: 14072 / % possible obs: 99.95 % / Redundancy: 2 % / Biso Wilson estimate: 48.39 Å2 / CC1/2: 1 / Net I/σ(I): 17.15
Reflection shellResolution: 2.19→2.269 Å / Num. unique obs: 1367 / CC1/2: 0.861

-
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: 2.19→45.75 Å / SU ML: 0.3632 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7477
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2531 701 4.98 %
Rwork0.2237 13368 -
obs0.225 14069 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.42 Å2
Refinement stepCycle: LAST / Resolution: 2.19→45.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1455 0 37 77 1569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00971512
X-RAY DIFFRACTIONf_angle_d1.39232038
X-RAY DIFFRACTIONf_chiral_restr0.0668226
X-RAY DIFFRACTIONf_plane_restr0.0049257
X-RAY DIFFRACTIONf_dihedral_angle_d15.1214575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.360.37511450.31722583X-RAY DIFFRACTION99.89
2.36-2.60.23991460.23832608X-RAY DIFFRACTION100
2.6-2.970.34811330.27992643X-RAY DIFFRACTION99.96
2.97-3.750.25871390.22852676X-RAY DIFFRACTION100
3.75-45.750.21641380.19652858X-RAY DIFFRACTION99.97
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)
14.832926102392.28972417091-0.2444519466972.11707768625-1.363211899912.35256411850.0877204680937-0.2456775907790.514597825595-0.106492413753-0.2621960303130.407276565062-0.300057025187-0.1709454023950.0003271901411140.4097423143510.0078751831809-0.03968814730830.66310530379-0.1458212608530.61149944408945.183287838850.648726625951.6809943284
22.840862338552.691327579851.287105209363.13959881868-0.1594406951543.652614367160.05463155455730.123867767318-0.351175816778-0.198252134670.0761412611452-0.6783301529560.1919685441760.6969206900420.002147235180530.4394195337670.0710748393-0.1187395282610.749536472064-0.1046059617390.5579128727741.998168042932.455322141644.8540404079
30.8049689623840.404777599220.6964903218330.4034540162110.2636254887640.7583080179810.494513767675-0.522165151830.0114671277505-0.276906060278-0.0110925690790.081737783737-0.4095802391420.1368152935010.0003310275611150.3709908508120.0705572766046-0.02932754298270.475016722345-0.1178499932110.48842399566836.378194157433.747345078342.0840723967
41.10365913665-0.1436254786481.129925503360.999878541797-0.05974383711971.138956447650.250155252844-0.295069498806-0.252131932949-0.07883569821890.1784779677-0.250058806988-0.03485395349710.7028162674382.42246667259E-60.510140857728-0.002619922204660.004157766450770.916871677772-0.280953856160.63124451683745.498281688236.512890233738.1555569458
53.983490285931.270327835681.663528841511.317798016711.314961297844.354429462650.202565363277-0.1594182678360.280558998830.162895379289-0.1715044875860.2469270296250.2871262797650.1699520341730.003770068432150.3000126844850.104885694898-0.07336338823390.526736590806-0.02156410080410.42337389342737.642729612635.434258377446.1157066389
68.038840328493.12797073920.3923173526514.724290837230.07945912161355.54460217422-0.1233822989560.395034469016-0.0499666807538-0.1331840586550.106512062398-0.262561652636-0.01822650286720.2603440026090.000760702978890.3205627003230.03278873245630.02984056687620.69026149162-0.124828016340.47922120676550.751984258846.008478982650.1176494578
71.999975268971.999985608352.000013909631.999980624882.000015529521.99998554717-1.394304493821.755982764840.647021559645-4.08558102151-1.131122436024.31940163486-3.942954141671.74062158392.529569507631.102928786480.269705935945-0.5735479934840.9481598199210.09702775795831.0592339457952.578120876826.995599297462.6109614876
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 69 )54 - 6953 - 68
44chain 'A' and (resid 70 through 89 )70 - 8969 - 88
55chain 'A' and (resid 90 through 127 )90 - 12789 - 126
66chain 'A' and (resid 128 through 176 )128 - 176127 - 175
77chain 'A' and (resid 177 through 177 )177176

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more