[English] 日本語
Yorodumi
- PDB-5mbd: Structure of a bacterial light-regulated adenylyl cylcase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mbd
TitleStructure of a bacterial light-regulated adenylyl cylcase
ComponentsBeta subunit of photoactivated adenylyl cyclase
KeywordsLYASE / BLUF / adenylyl cyclase / photoreceptor / optogenetics
Function / homology
Function and homology information


cyclic nucleotide biosynthetic process / blue light photoreceptor activity / adenylate cyclase activity / FAD binding / cell projection / intracellular signal transduction / ATP binding / metal ion binding
Similarity search - Function
BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / Sensors of blue-light using FAD / Acylphosphatase-like domain superfamily / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Beta subunit of photoactivated adenylyl cyclase
Similarity search - Component
Biological speciesBeggiatoa sp. PS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLindner, R. / Hartmann, E. / Tarnawski, M. / Winkler, A. / Frey, D. / Reinstein, J. / Meinhart, A. / Schlichting, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationFOR1279 Germany
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Photoactivation Mechanism of a Bacterial Light-Regulated Adenylyl Cyclase.
Authors: Lindner, R. / Hartmann, E. / Tarnawski, M. / Winkler, A. / Frey, D. / Reinstein, J. / Meinhart, A. / Schlichting, I.
History
DepositionNov 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 2.0Jan 17, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta subunit of photoactivated adenylyl cyclase
B: Beta subunit of photoactivated adenylyl cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2366
Polymers80,2532
Non-polymers9844
Water2,270126
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-102 kcal/mol
Surface area30070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.700, 56.710, 77.730
Angle α, β, γ (deg.)104.650, 103.860, 102.720
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Beta subunit of photoactivated adenylyl cyclase


Mass: 40126.441 Da / Num. of mol.: 2 / Fragment: Beggiatoa photoactivatable adenylyl cyclase bPAC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beggiatoa sp. PS (bacteria) / Gene: BGP_1043 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7BT71
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M Na-MES pH 6.5, 0.6 M NaCl, 20 % w/v PEG 3350; 0.3 mM alpha,beta-methylene-ATP in drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2011
RadiationMonochromator: DOUBLE-CRYSTAL Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→44.3 Å / Num. obs: 33433 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 38.44 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.43
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.25-2.350.5073.28195.1
2.35-2.40.3964.04195.9
2.4-2.50.3594.88196.5
2.5-2.60.2885.59196.6
2.6-2.70.227.19196.4
2.7-30.1528.99197
3-40.06416.05196.7
4-50.0422.24195.4
5-60.04123.14196.3
6-100.03523.14195.5
100.02926.4197.5

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M27

5m27


Resolution: 2.25→44.289 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2172 980 2.93 %
Rwork0.1895 32453 -
obs0.1903 33433 96.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.78 Å2 / Biso mean: 51.7839 Å2 / Biso min: 15.67 Å2
Refinement stepCycle: final / Resolution: 2.25→44.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5417 0 64 126 5607
Biso mean--77.36 46.56 -
Num. residues----678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045596
X-RAY DIFFRACTIONf_angle_d0.6897587
X-RAY DIFFRACTIONf_chiral_restr0.044898
X-RAY DIFFRACTIONf_plane_restr0.004941
X-RAY DIFFRACTIONf_dihedral_angle_d15.5253385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.36860.29661340.26014581471595
2.3686-2.5170.27031410.24164658479996
2.517-2.71130.29051400.2264621476197
2.7113-2.98410.25841400.21264699483997
2.9841-3.41580.23011430.19174654479797
3.4158-4.3030.20641390.16724591473096
4.303-44.29790.16791430.16684649479297
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)
10.5099-0.16180.44260.69030.08621.33850.13610.0973-0.1873-0.0943-0.0369-0.01590.2946-0.0576-00.36-0.0319-0.01370.2951-0.0330.1456-21.3571-19.2642-37.352
21.50140.5358-0.18570.8169-0.17810.04680.0991-0.2016-0.1350.0189-0.073-0.0607-0.0062-0.0096-00.15530.0053-0.01480.1591-0.01940.1794-15.574-17.99941.4219
30.353-0.1158-0.58710.46920.46761.37490.02720.01260.1258-0.21350.00530.0244-0.40970.315600.4611-0.0728-0.00760.47280.0770.1979-11.04774.4427-38.3686
41.36660.3970.08391.20550.3079-0.02070.0102-0.14230.19020.02030.00910.06070.0185-0.0005-00.14130.01620.01330.16020.02160.1751-17.74857.57061.7703
50.0045-0.0051-0.01660.014-0.0220.0436-0.3282-0.09570.15190.030.03390.26020.1369-0.1196-00.3076-0.0332-0.01360.3174-0.02240.2433-27.9258-9.9689-19.3115
60.03020.00320.01660.0172-0.01370.0274-0.14470.2187-0.055-0.03980.11260.03290.10440.0298-00.3225-0.01820.02380.32580.00360.2173-5.2602-2.2895-19.1377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 126 )A2 - 126
2X-RAY DIFFRACTION2chain 'A' and (resid 147 through 347 )A147 - 347
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 126 )B2 - 126
4X-RAY DIFFRACTION4chain 'B' and (resid 147 through 347 )B147 - 347
5X-RAY DIFFRACTION5chain 'A' and (resid 127 through 146 )A127 - 146
6X-RAY DIFFRACTION6chain 'B' and (resid 127 through 146 )B127 - 146

+
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