[English] 日本語
Yorodumi
- PDB-8qfe: Cryogenic crystal structure of the Photoactivated Adenylate Cycla... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8qfe
TitleCryogenic crystal structure of the Photoactivated Adenylate Cyclase OaPAC
ComponentsFamily 3 adenylate cyclase
KeywordsLYASE / Photoreceptor / BLUF / Adenylate Cyclase / PAC
Function / homology
Function and homology information


blue light photoreceptor activity / cAMP biosynthetic process / adenylate cyclase activity / FAD binding / 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 / Family 3 adenylate cyclase
Similarity search - Component
Biological speciesOscillatoria acuminata PCC 6304 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChretien, A. / Nagel, M.F. / Botha, S. / de Wijn, R. / Brings, L. / Doerner, K. / Han, H. / Koliyadu, J. / Letrun, R. / Round, A. ...Chretien, A. / Nagel, M.F. / Botha, S. / de Wijn, R. / Brings, L. / Doerner, K. / Han, H. / Koliyadu, J. / Letrun, R. / Round, A. / Sato, T. / Schmidt, C. / Secareanu, R. / von Stetten, D. / Vakili, M. / Wrona, A. / Bean, R. / Mancuso, A. / Schulz, J. / Pearson, A. / Kottke, T. / Lorenzen, K. / Schubert, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: J.Mol.Biol. / Year: 2024
Title: Light-induced Trp in /Met out Switching During BLUF Domain Activation in ATP-bound Photoactivatable Adenylate Cyclase OaPAC.
Authors: Chretien, A. / Nagel, M.F. / Botha, S. / de Wijn, R. / Brings, L. / Dorner, K. / Han, H. / Koliyadu, J.C.P. / Letrun, R. / Round, A. / Sato, T. / Schmidt, C. / Secareanu, R.C. / von Stetten, ...Authors: Chretien, A. / Nagel, M.F. / Botha, S. / de Wijn, R. / Brings, L. / Dorner, K. / Han, H. / Koliyadu, J.C.P. / Letrun, R. / Round, A. / Sato, T. / Schmidt, C. / Secareanu, R.C. / von Stetten, D. / Vakili, M. / Wrona, A. / Bean, R. / Mancuso, A. / Schulz, J. / Pearson, A.R. / Kottke, T. / Lorenzen, K. / Schubert, R.
History
DepositionSep 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 13, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Family 3 adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7733
Polymers39,2931
Non-polymers4812
Water5,909328
1
A: Family 3 adenylate cyclase
hetero molecules
x 5
A: Family 3 adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,64118
Polymers235,7576
Non-polymers2,88412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
Unit cell
Length a, b, c (Å)52.856, 146.202, 103.595
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-690-

HOH

21A-700-

HOH

31A-767-

HOH

-
Components

#1: Protein Family 3 adenylate cyclase


Mass: 39292.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oscillatoria acuminata PCC 6304 (bacteria)
Gene: Oscil6304_3613 / Production host: Escherichia coli (E. coli) / References: UniProt: K9TLZ5
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 50% protein at 10 mg/mL : 50 mM TRIS/HCl pH 8.5, 50 mM sodium chloride, 5 mM ATP 50% crystallization buffer : 100 mM SPG buffer pH 7.0, 1.2 M disodium succinate, 100 mM guanidine ...Details: 50% protein at 10 mg/mL : 50 mM TRIS/HCl pH 8.5, 50 mM sodium chloride, 5 mM ATP 50% crystallization buffer : 100 mM SPG buffer pH 7.0, 1.2 M disodium succinate, 100 mM guanidine hydrochloride, 5 mM magnesium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Feb 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.5→33.86 Å / Num. obs: 64596 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 21.64 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.021 / Rrim(I) all: 0.055 / Χ2: 1.04 / Net I/σ(I): 25
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3212 / CC1/2: 0.846 / Χ2: 0.8 / % possible all: 100

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
PHENIX1.20.1_4487refinement
Coot0.9.8.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→31.22 Å / SU ML: 0.1539 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.8807
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1887 3164 4.9 %
Rwork0.1643 61379 -
obs0.1655 64543 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.5 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 32 328 3072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01283214
X-RAY DIFFRACTIONf_angle_d1.18564415
X-RAY DIFFRACTIONf_chiral_restr0.0688499
X-RAY DIFFRACTIONf_plane_restr0.0122590
X-RAY DIFFRACTIONf_dihedral_angle_d5.6817477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.2911390.26032636X-RAY DIFFRACTION99.96
1.52-1.550.30531480.24182630X-RAY DIFFRACTION99.93
1.55-1.570.28331130.22632647X-RAY DIFFRACTION100
1.57-1.60.26151140.21492664X-RAY DIFFRACTION100
1.6-1.630.23471160.20322663X-RAY DIFFRACTION100
1.63-1.660.24211330.19972676X-RAY DIFFRACTION99.96
1.66-1.690.2291450.20552599X-RAY DIFFRACTION99.96
1.69-1.730.26711350.20692662X-RAY DIFFRACTION100
1.73-1.770.23361410.18992646X-RAY DIFFRACTION99.96
1.77-1.810.24111250.17612651X-RAY DIFFRACTION99.89
1.81-1.860.20271540.17292608X-RAY DIFFRACTION100
1.86-1.920.20851270.15842671X-RAY DIFFRACTION99.96
1.92-1.980.1821450.162652X-RAY DIFFRACTION99.96
1.98-2.050.22081640.17332643X-RAY DIFFRACTION99.96
2.05-2.130.1921200.16642662X-RAY DIFFRACTION100
2.13-2.230.18761620.14592656X-RAY DIFFRACTION100
2.23-2.350.181210.14582693X-RAY DIFFRACTION100
2.35-2.490.17711350.15492679X-RAY DIFFRACTION100
2.49-2.690.17521330.14922684X-RAY DIFFRACTION100
2.69-2.960.1631620.15852676X-RAY DIFFRACTION99.96
2.96-3.380.19751310.15932721X-RAY DIFFRACTION100
3.38-4.260.12741370.1422728X-RAY DIFFRACTION100
4.26-31.220.20611640.17562832X-RAY DIFFRACTION99.57
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)
10.381565221238-0.1381342035670.06487041858671.3812567356-0.9616532652281.394760736690.00905708409263-0.0951177693921-0.0520810414588-0.05076752553980.07607311050220.1029418106830.219544347957-0.0605947582485-0.08098545777210.322380176374-0.0250296921007-0.01004674525160.2597587686070.007064538308570.155711599846-3.99897212165-7.65703681577-14.4981202866
20.451724540043-0.0286008835469-0.003802478968351.110350052440.4930898745091.438483841530.051036263679-0.03332604080810.109644805950.0459467303998-0.01196362572520.0108953794083-0.134126694401-0.0495489264919-0.02653637263460.2196405732190.005197450876210.01082640947920.2178390537360.002875256375630.12495952205-2.7618210852928.8607456232-14.1266979307
30.6201665687740.0901304699827-2.305048184917.890745898-0.09015519042828.59143538085-0.0597413955295-0.008908292033331.00466313759-0.2179412847630.148458916470.0245546026913-1.66757762348-0.28375379865-0.002800890553940.913047759818-0.156051051471-0.1226193095910.753580861247-0.1242425963590.75943149322812.821018395538.5366649686-7.10048428641
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 1 through 146 )1 - 1461 - 146
22chain 'A' and (resid 147 through 327 )147 - 327147 - 327
33chain 'A' and (resid 328 through 350 )328 - 350328 - 350

+
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