[English] 日本語
Yorodumi
- PDB-8c4p: CdaA-compound 7 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8c4p
TitleCdaA-compound 7 complex
ComponentsDiadenylate cyclase
KeywordsPROTEIN BINDING / Complex
Function / homology
Function and homology information


diadenylate cyclase activity / diadenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / ATP binding / plasma membrane
Similarity search - Function
Diadenylate cyclase CdaA, N-terminal domain / CdaA N-terminal transmembrane domain / Diadenylate cyclase CdaA / Diadenylate cyclase / DNA integrity scanning protein, DisA, N-terminal / DNA integrity scanning protein, DisA, N-terminal domain superfamily / DisA bacterial checkpoint controller nucleotide-binding / Diadenylate cyclase (DAC) domain profile.
Similarity search - Domain/homology
Chem-TJ9 / Diadenylate cyclase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å
AuthorsNeumann, P. / Ficner, R.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP1879 Germany
German Research Foundation (DFG)SFB860 Germany
CitationJournal: Microlife / Year: 2023
Title: Computer-aided design of a cyclic di-AMP synthesizing enzyme CdaA inhibitor.
Authors: Neumann, P. / Kloskowski, P. / Ficner, R.
History
DepositionJan 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.country

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diadenylate cyclase
B: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,74318
Polymers38,7382
Non-polymers1,00516
Water8,647480
1
A: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,94311
Polymers19,3691
Non-polymers57310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8017
Polymers19,3691
Non-polymers4326
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.760, 64.200, 128.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Diadenylate cyclase / DAC / Cyclic-di-AMP synthase / c-di-AMP synthase / Diadenylate cyclase CdaA


Mass: 19369.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: dacA, cdaA, lmo2120 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y5E4, diadenylate cyclase
#2: Chemical ChemComp-TJ9 / ~{N}-[5-(2-azanyl-1,3-thiazol-4-yl)-4-methyl-1,3-thiazol-2-yl]ethanamide


Mass: 254.332 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10N4OS2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 3.7 M NaCl, 0.1M Na-HEPES pH 8.5 and 3 % DMSO

-
Data collection

DiffractionMean temperature: 180 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.977 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 203653 / % possible obs: 97.3 % / Redundancy: 8 % / Biso Wilson estimate: 15.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.051 / Net I/σ(I): 13.92
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.2-1.251.201212880.4111.4821
1.25-1.310.959214450.5911.1141
1.31-1.420.71345690.8590.7721
1.42-80.0421256340.9990.0461
8-140.0275830.9980.0291
14-170.028580.9990.031
17-500.028760.9980.0321

-
Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.2→45.46 Å / SU ML: 0.1386 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 19.1552
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1622 10165 5 %
Rwork0.1388 193317 -
obs0.1399 203482 97.25 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.75 Å2
Refinement stepCycle: LAST / Resolution: 1.2→45.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 0 46 480 3139
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692886
X-RAY DIFFRACTIONf_angle_d0.90453928
X-RAY DIFFRACTIONf_chiral_restr0.0839451
X-RAY DIFFRACTIONf_plane_restr0.0079509
X-RAY DIFFRACTIONf_dihedral_angle_d12.92041108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.33172510.34134732X-RAY DIFFRACTION71.09
1.21-1.230.32272790.33125313X-RAY DIFFRACTION80.07
1.23-1.240.33352930.32385530X-RAY DIFFRACTION84.54
1.24-1.260.30263190.30016075X-RAY DIFFRACTION90.91
1.26-1.280.323240.29336256X-RAY DIFFRACTION94.7
1.28-1.290.31123340.27546477X-RAY DIFFRACTION97.79
1.29-1.310.27713420.2526609X-RAY DIFFRACTION99.37
1.31-1.330.25933490.23146574X-RAY DIFFRACTION99.91
1.33-1.350.243470.21216711X-RAY DIFFRACTION99.92
1.35-1.370.21743490.19376519X-RAY DIFFRACTION99.99
1.37-1.40.23463520.18286690X-RAY DIFFRACTION100
1.4-1.420.21063450.17276636X-RAY DIFFRACTION99.96
1.42-1.450.22583510.16056586X-RAY DIFFRACTION99.96
1.45-1.480.19383490.14686635X-RAY DIFFRACTION100
1.48-1.510.17683490.13526588X-RAY DIFFRACTION99.97
1.51-1.550.15913610.12866665X-RAY DIFFRACTION99.9
1.55-1.590.17423450.12056549X-RAY DIFFRACTION99.88
1.59-1.630.16393500.11986684X-RAY DIFFRACTION99.94
1.63-1.680.16223480.11736603X-RAY DIFFRACTION99.96
1.68-1.730.15553500.10946642X-RAY DIFFRACTION99.91
1.73-1.790.15183560.10976590X-RAY DIFFRACTION99.96
1.79-1.860.16263400.11596635X-RAY DIFFRACTION100
1.86-1.950.17443460.11486648X-RAY DIFFRACTION100
1.95-2.050.15783510.11056618X-RAY DIFFRACTION100
2.05-2.180.14283510.11146620X-RAY DIFFRACTION100
2.18-2.350.14033520.11646622X-RAY DIFFRACTION100
2.35-2.590.15553430.12516603X-RAY DIFFRACTION100
2.59-2.960.14663530.14096642X-RAY DIFFRACTION100
2.96-3.730.12133490.12686626X-RAY DIFFRACTION100
3.73-45.460.15563370.14086639X-RAY DIFFRACTION99.97

+
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://pdbjlvh1.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