[English] 日本語
Yorodumi
- PDB-7d48: apo-form cyclic trinucleotide synthase CdnD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d48
Titleapo-form cyclic trinucleotide synthase CdnD
ComponentsCyclic AMP-AMP-GMP synthase
KeywordsTRANSFERASE / cyclic trinucleotide synthesis nucleotidyl transferase
Function / homology
Function and homology information


nucleotide metabolic process / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / GTP binding / ATP binding / metal ion binding
Similarity search - Function
Second Messenger Oligonucleotide or Dinucleotide Synthetase domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Cyclic AMP-AMP-GMP synthase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsYang, C.-S. / Hou, M.-H. / Tsai, C.-L. / Wang, Y.-C. / Ko, T.-P. / Chen, Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Crystal structure and functional implication of a bacterial cyclic AMP-AMP-GMP synthetase.
Authors: Ko, T.P. / Wang, Y.C. / Tsai, C.L. / Yang, C.S. / Hou, M.H. / Chen, Y.
History
DepositionSep 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 19, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclic AMP-AMP-GMP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4022
Polymers44,3791
Non-polymers231
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area16580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.924, 52.924, 344.361
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
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-649-

HOH

21A-865-

HOH

31A-869-

HOH

-
Components

#1: Protein Cyclic AMP-AMP-GMP synthase / cGAS/DncV-like nucleotidyltransferase / CD-NTase


Mass: 44378.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Na is a sodium ion / Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: cdnD02, P853_02262
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0DSP4, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 8% v/v Tacsimate, pH 6.0, 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.14→30 Å / Num. obs: 27647 / % possible obs: 98.9 % / Redundancy: 8.7 % / Biso Wilson estimate: 27.98 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 17
Reflection shellResolution: 2.14→2.22 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.7 / % possible all: 97.5

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Blu-Icedata collection
HKL-2000data processing
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→24.01 Å / SU ML: 0.201 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.513 / Stereochemistry target values: GEOSTD + MONOMER LIBRARY
RfactorNum. reflection% reflection
Rfree0.228 1211 5 %
Rwork0.182 --
obs0.185 24213 86.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.64 Å2
Refinement stepCycle: LAST / Resolution: 2.15→24.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2865 0 1 371 3237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032952
X-RAY DIFFRACTIONf_angle_d0.5934012
X-RAY DIFFRACTIONf_dihedral_angle_d14.6611774
X-RAY DIFFRACTIONf_chiral_restr0.04427
X-RAY DIFFRACTIONf_plane_restr0.005523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.240.3062670.2131283X-RAY DIFFRACTION45
2.24-2.340.265880.20111659X-RAY DIFFRACTION58
2.34-2.470.26911250.20262367X-RAY DIFFRACTION83
2.47-2.620.24641500.20452860X-RAY DIFFRACTION99
2.62-2.820.28171530.20382907X-RAY DIFFRACTION100
2.82-3.110.24511550.20342940X-RAY DIFFRACTION100
3.11-3.550.22941540.17892932X-RAY DIFFRACTION100
3.55-4.470.20111560.15742964X-RAY DIFFRACTION99
4.47-24.010.19651630.1713090X-RAY DIFFRACTION96
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)
1-0.2613-0.07020.12090.24370.10330.4584-0.0685-0.14160.11730.1380.05410.0729-0.1384-0.05370.01910.16960.0054-0.00360.2834-0.02150.159945.125145.3316156.7013
20.1708-0.0371-0.05480.28950.26820.7557-0.04360.0857-0.06910.2398-0.0311-0.06140.19050.2608-0.00150.19950.03020.00080.3024-0.04280.213453.742633.8265162.1937
30.04070.01-0.05450.0123-0.02110.0406-0.0558-0.20170.49460.10140.20970.1717-0.2479-0.36610.00410.30660.0147-0.01770.5148-0.14520.484561.429757.4272155.3639
40.8802-0.36340.2780.11590.09420.8488-0.29820.26570.30180.0926-0.0896-0.22830.1440.9419-0.3094-0.04930.07750.04730.397-0.0690.194359.533439.8775148.7749
50.6097-0.06540.21630.466-0.5580.87320.0237-0.05080.0271-0.1089-0.06820.0363-0.04320.1964-0.08690.03320.00450.00780.1525-0.02730.119141.658842.763133.7543
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 76 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 77 THROUGH 154 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 155 THROUGH 174 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 175 THROUGH 223 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 224 THROUGH 355 )

+
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