[English] 日本語
Yorodumi
- PDB-4rv7: Characterization of an essential diadenylate cyclase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rv7
TitleCharacterization of an essential diadenylate cyclase
ComponentsDiadenylate cyclase
KeywordsTRANSFERASE / DAC-fold / ATP binding / c-di-AMP binding
Function / homology
Function and homology information


diadenylate cyclase activity / diadenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / ATP binding / plasma membrane
Similarity search - Function
YojJ-like (1 / DNA integrity scanning protein, DisA, N-terminal domain / 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. ...YojJ-like (1 / DNA integrity scanning protein, DisA, N-terminal domain / 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. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / HEXANE-1,6-DIOL / Diadenylate cyclase
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDickmanns, A. / Neumann, P. / Ficner, R.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural and Biochemical Analysis of the Essential Diadenylate Cyclase CdaA from Listeria monocytogenes.
Authors: Rosenberg, J. / Dickmanns, A. / Neumann, P. / Gunka, K. / Arens, J. / Kaever, V. / Stulke, J. / Ficner, R. / Commichau, F.M.
History
DepositionNov 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 4, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rsym_value
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,24713
Polymers84,0034
Non-polymers2,2449
Water543
1
A: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6504
Polymers21,0011
Non-polymers6503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5323
Polymers21,0011
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5323
Polymers21,0011
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5323
Polymers21,0011
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.680, 130.680, 178.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 3:35 or resseq 44:152 or resseq...
21chain B and (resseq 3:35 or resseq 44:152 or resseq...
31chain C and (resseq 3:35 or resseq 44:152 or resseq...
41chain D and (resseq 3:35 or resseq 44:152 or resseq...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERALAALAchain A and (resseq 3:35 or resseq 44:152 or resseq...AA3 - 3522 - 54
12ILEILEGLUGLUchain A and (resseq 3:35 or resseq 44:152 or resseq...AA44 - 15263 - 171
13ATPATPATPATPchain A and (resseq 3:35 or resseq 44:152 or resseq...AE1001
21SERSERALAALAchain B and (resseq 3:35 or resseq 44:152 or resseq...BB3 - 3522 - 54
22ILEILEGLUGLUchain B and (resseq 3:35 or resseq 44:152 or resseq...BB44 - 15263 - 171
23ATPATPATPATPchain B and (resseq 3:35 or resseq 44:152 or resseq...BH1001
31SERSERALAALAchain C and (resseq 3:35 or resseq 44:152 or resseq...CC3 - 3522 - 54
32ILEILEGLUGLUchain C and (resseq 3:35 or resseq 44:152 or resseq...CC44 - 15263 - 171
33ATPATPATPATPchain C and (resseq 3:35 or resseq 44:152 or resseq...CJ1001
41SERSERALAALAchain D and (resseq 3:35 or resseq 44:152 or resseq...DD3 - 3522 - 54
42ILEILEGLUGLUchain D and (resseq 3:35 or resseq 44:152 or resseq...DD44 - 15263 - 171
43ATPATPATPATPchain D and (resseq 3:35 or resseq 44:152 or resseq...DL1001

NCS oper:
IDCodeMatrixVector
1given(0.160524, 0.824121, 0.543192), (0.882137, 0.127098, -0.45352), (-0.442794, 0.55197, -0.706585)36.1171, -71.906097, 34.603199
2given(0.107322, 0.880103, -0.462495), (0.822149, 0.183017, 0.539051), (0.559065, -0.438091, -0.703934)72.230103, -35.468899, -26.4676
3given(0.495519, 0.502494, -0.708492), (0.493988, 0.507886, 0.705711), (0.714448, -0.69968, 0.003442)0.283212, -65.037003, -45.916

-
Components

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


Mass: 21000.807 Da / Num. of mol.: 4 / Fragment: UNP residues 151-273
Source method: isolated from a genetically manipulated source
Details: N-terminal Strep TAG
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: dacA, lmo2120 / Plasmid: pBP33 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y5E4, diadenylate cyclase
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.53 Å3/Da / Density % sol: 72.83 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 6-16 % 1,6 Hexanediol, 2 mM Spermine, 20 mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.77318 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2013 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77318 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 38360 / Num. obs: 38360 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 78.97 Å2 / Rmerge(I) obs: 0.051 / Χ2: 0.985 / Net I/σ(I): 24.42
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.8-2.940.6812.74338745240199.7
2.94-3.090.4734.13299764341199.6
3.09-3.370.2387.67444286604199.5
3.37-3.910.09117.97515327858199.3
3.91-4.180.04832.86172262552199.3
4.18-4.450.03641.92129671974198.8
4.45-4.720.03143.8791011538198.4
4.72-140.02157.31505457906198.2
14-170.01477.84775157197.5
17-500.01670617190186.8

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
DNAdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FB5

2fb5


Resolution: 2.8→48.864 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 0 / Phase error: 27.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2562 1918 5 %Random, thin shells
Rwork0.2399 ---
obs0.2407 38331 99.16 %-
all-38360 --
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 329.42 Å2 / Biso mean: 88.1814 Å2 / Biso min: 36.85 Å2
Refine analyzeLuzzati sigma a free: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.8→48.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4852 0 136 3 4991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045055
X-RAY DIFFRACTIONf_angle_d0.8896860
X-RAY DIFFRACTIONf_chiral_restr0.057816
X-RAY DIFFRACTIONf_plane_restr0.003850
X-RAY DIFFRACTIONf_dihedral_angle_d16.6651901
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1015X-RAY DIFFRACTIONPOSITIONAL0.013
12B1015X-RAY DIFFRACTIONPOSITIONAL0.013
13C1017X-RAY DIFFRACTIONPOSITIONAL0.015
14D1018X-RAY DIFFRACTIONPOSITIONAL0.017
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.870.32781360.325325662702100
2.87-2.94760.33491350.311125592694100
2.9476-3.03430.34251350.317725742709100
3.0343-3.13230.34991350.302625702705100
3.1323-3.24420.33521360.293825682704100
3.2442-3.37410.28371350.27892566270199
3.3741-3.52760.2661360.2712590272699
3.5276-3.71350.34781360.27592582271899
3.7135-3.94610.27011370.243426092746100
3.9461-4.25060.22311370.21212593273099
4.2506-4.6780.23371360.2042600273699
4.678-5.35420.21491390.21742632277199
5.3542-6.74290.23041390.2322639277898
6.7429-48.8710.23131460.21992765291197
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)
11.81541.0443-0.21143.73330.20192.03530.1003-0.20690.00670.1823-0.14540.22740.047-0.265-0.02390.4091-0.08920.00020.64830.01950.374-10.1051-63.54537.8502
21.66231.5988-0.30382.57431.06091.80840.04050.05520.1698-0.20920.0426-0.2695-0.37530.01520.02010.684-0.07140.00480.5980.07630.483511.7883-51.9113-10.0141
32.77591.4486-0.02681.472-0.44920.2610.01850.2804-0.4781-0.274-0.04-0.4455-0.090.25130.0990.6569-0.1157-0.02620.55780.06670.7106-12.3983-92.4563-1.5118
41.31490.63951.15872.18150.06551.30530.3037-0.1955-0.40050.2661-0.1147-0.43-0.03380.02440.18740.5381-0.2225-0.08140.60730.17350.683733.55-42.06958.6793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA-1 - 1001
2X-RAY DIFFRACTION2chain BB0 - 1001
3X-RAY DIFFRACTION3chain CC-3 - 1001
4X-RAY DIFFRACTION4chain DD1 - 1001

+
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