[English] 日本語
Yorodumi
- PDB-6saw: Chromophore binding domain of bacteriophytochrome linked diguanyl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6saw
TitleChromophore binding domain of bacteriophytochrome linked diguanylyl cyclase from Idiomarina species A28L (dimeric Pfr-like state).
ComponentsDiguanylate cyclase (GGDEF) domain-containing protein
KeywordsLYASE / bacteriophytochrome / biliverdin / activated conformation
Function / homology
Function and homology information


diguanylate cyclase / diguanylate cyclase activity / detection of visible light / photoreceptor activity / regulation of DNA-templated transcription / GTP binding / metal ion binding
Similarity search - Function
: / Phytochrome / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GAF domain / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region ...: / Phytochrome / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GAF domain / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LBV / diguanylate cyclase
Similarity search - Component
Biological speciesIdiomarina sp. A28L (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsGourinchas, G. / Winkler, A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP32022 Austria
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Distinct chromophore-protein environments enable asymmetric activation of a bacteriophytochrome-activated diguanylate cyclase.
Authors: Buhrke, D. / Gourinchas, G. / Muller, M. / Michael, N. / Hildebrandt, P. / Winkler, A.
History
DepositionJul 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diguanylate cyclase (GGDEF) domain-containing protein
B: Diguanylate cyclase (GGDEF) domain-containing protein
C: Diguanylate cyclase (GGDEF) domain-containing protein
D: Diguanylate cyclase (GGDEF) domain-containing protein
E: Diguanylate cyclase (GGDEF) domain-containing protein
F: Diguanylate cyclase (GGDEF) domain-containing protein
G: Diguanylate cyclase (GGDEF) domain-containing protein
H: Diguanylate cyclase (GGDEF) domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,16724
Polymers287,1988
Non-polymers4,96916
Water1448
1
A: Diguanylate cyclase (GGDEF) domain-containing protein
hetero molecules

C: Diguanylate cyclase (GGDEF) domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0426
Polymers71,8002
Non-polymers1,2424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area4900 Å2
ΔGint-56 kcal/mol
Surface area28330 Å2
MethodPISA
2
B: Diguanylate cyclase (GGDEF) domain-containing protein
hetero molecules

E: Diguanylate cyclase (GGDEF) domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0426
Polymers71,8002
Non-polymers1,2424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area4900 Å2
ΔGint-62 kcal/mol
Surface area28010 Å2
MethodPISA
3
D: Diguanylate cyclase (GGDEF) domain-containing protein
G: Diguanylate cyclase (GGDEF) domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0426
Polymers71,8002
Non-polymers1,2424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-62 kcal/mol
Surface area28490 Å2
MethodPISA
4
F: Diguanylate cyclase (GGDEF) domain-containing protein
H: Diguanylate cyclase (GGDEF) domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0426
Polymers71,8002
Non-polymers1,2424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-58 kcal/mol
Surface area28260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)344.650, 344.650, 92.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 6 through 192 or resid 194 through 312))
21(chain B and (resid 6 through 192 or resid 194 through 312))
31(chain C and (resid 6 through 192 or resid 194 through 312))
41(chain D and (resid 6 through 192 or resid 194 through 312))
51(chain E and (resid 6 through 192 or resid 194 through 312))
61(chain F and (resid 6 through 192 or resid 194 through 312))
71(chain G and (resid 6 through 192 or resid 194 through 312))
81(chain H and (resid 6 through 192 or resid 194 through 312))

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
11GLYGLYASNASN(chain A and (resid 6 through 192 or resid 194 through 312))AA6 - 1928 - 194
12HISHISHISHIS(chain A and (resid 6 through 192 or resid 194 through 312))AA194 - 312196 - 314
21GLYGLYASNASN(chain B and (resid 6 through 192 or resid 194 through 312))BB6 - 1928 - 194
22HISHISHISHIS(chain B and (resid 6 through 192 or resid 194 through 312))BB194 - 312196 - 314
31GLYGLYASNASN(chain C and (resid 6 through 192 or resid 194 through 312))CC6 - 1928 - 194
32HISHISHISHIS(chain C and (resid 6 through 192 or resid 194 through 312))CC194 - 312196 - 314
41GLYGLYASNASN(chain D and (resid 6 through 192 or resid 194 through 312))DD6 - 1928 - 194
42HISHISHISHIS(chain D and (resid 6 through 192 or resid 194 through 312))DD194 - 312196 - 314
51GLYGLYASNASN(chain E and (resid 6 through 192 or resid 194 through 312))EE6 - 1928 - 194
52HISHISHISHIS(chain E and (resid 6 through 192 or resid 194 through 312))EE194 - 312196 - 314
61GLYGLYASNASN(chain F and (resid 6 through 192 or resid 194 through 312))FF6 - 1928 - 194
62HISHISHISHIS(chain F and (resid 6 through 192 or resid 194 through 312))FF194 - 312196 - 314
71GLYGLYASNASN(chain G and (resid 6 through 192 or resid 194 through 312))GG6 - 1928 - 194
72HISHISHISHIS(chain G and (resid 6 through 192 or resid 194 through 312))GG194 - 312196 - 314
81GLYGLYASNASN(chain H and (resid 6 through 192 or resid 194 through 312))HH6 - 1928 - 194
82HISHISHISHIS(chain H and (resid 6 through 192 or resid 194 through 312))HH194 - 312196 - 314

-
Components

#1: Protein
Diguanylate cyclase (GGDEF) domain-containing protein


Mass: 35899.766 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Idiomarina sp. A28L (bacteria) / Gene: A28LD_0430 / Plasmid: pETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F7RW09
#2: Chemical
ChemComp-LBV / 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid / 2(R),3(E)- PHYTOCHROMOBILIN


Mass: 585.670 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C33H37N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.69 Å3/Da / Density % sol: 66.67 % / Description: plate
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Bis-Tris pH6.5, 20 % PEG 5000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0047 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0047 Å / Relative weight: 1
ReflectionResolution: 3→55.023 Å / Num. obs: 81556 / % possible obs: 99.5 % / Redundancy: 3.484 % / Biso Wilson estimate: 53.238 Å2 / CC1/2: 0.956 / Rmerge(I) obs: 0.286 / Rrim(I) all: 0.338 / Χ2: 0.888 / Net I/σ(I): 4.94 / Num. measured all: 284153 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3-3.13.4021.3921.1225952767676290.2681.65699.4
3.1-3.23.3871.1571.4522764676667210.3991.3899.3
3.2-3.33.5560.9461.9121132597159420.5321.12499.5
3.3-3.43.5280.7722.4618346524452000.6410.91999.2
3.4-3.63.4670.5623.2730567888188170.790.66899.3
3.6-43.4170.4344.354363612838127690.8490.51699.5
4-63.5610.2027.138643224328242690.960.23899.8
6-103.4970.1189.1728042804080180.9860.13999.7
10-203.3490.07613.226470193819320.9870.08999.7
20-55.0233.1350.08114.218122792590.9810.09992.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.8 Å58.06 Å
Translation2.8 Å58.06 Å

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.1phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6et7

6et7


Resolution: 3→55.023 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 26.97
RfactorNum. reflection% reflection
Rfree0.2292 4077 5 %
Rwork0.1965 --
obs0.1982 81534 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 178.93 Å2 / Biso mean: 67.0715 Å2 / Biso min: 33.92 Å2
Refinement stepCycle: final / Resolution: 3→55.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19896 0 352 8 20256
Biso mean--67.51 68.45 -
Num. residues----2456
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A12220X-RAY DIFFRACTION8.43TORSIONAL
12B12220X-RAY DIFFRACTION8.43TORSIONAL
13C12220X-RAY DIFFRACTION8.43TORSIONAL
14D12220X-RAY DIFFRACTION8.43TORSIONAL
15E12220X-RAY DIFFRACTION8.43TORSIONAL
16F12220X-RAY DIFFRACTION8.43TORSIONAL
17G12220X-RAY DIFFRACTION8.43TORSIONAL
18H12220X-RAY DIFFRACTION8.43TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3-3.03520.46921400.4503263999
3.0352-3.07230.41331420.4215269399
3.0723-3.11110.43921400.41152669100
3.1111-3.15210.42911390.3634264099
3.1521-3.19520.32721430.3283272999
3.1952-3.24090.33731370.3183260899
3.2409-3.28930.33841410.30532676100
3.2893-3.34060.3251410.3253266799
3.3406-3.39540.36321410.3297267999
3.3954-3.4540.34891400.30412665100
3.454-3.51670.30561390.2586263199
3.5167-3.58440.29961420.2462269799
3.5844-3.65750.27221410.2328268199
3.6575-3.7370.26151390.2287264299
3.737-3.82390.25231400.22142670100
3.8239-3.91960.25211410.20282668100
3.9196-4.02550.20441430.18712711100
4.0255-4.14390.22481380.1732631100
4.1439-4.27760.19751410.15482683100
4.2776-4.43040.17291420.14132697100
4.4304-4.60770.16091410.13642675100
4.6077-4.81730.16951410.14192677100
4.8173-5.07110.17421400.14592661100
5.0711-5.38860.18691420.15132702100
5.3886-5.80430.21351410.16192680100
5.8043-6.38760.20411410.16372680100
6.3876-7.310.18871410.1592664100
7.31-9.20290.15651410.12882683100
9.2029-55.0230.15331390.1417265999

+
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