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- PDB-6saw: Chromophore binding domain of bacteriophytochrome linked diguanyl... -

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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 / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / GAF domain ...: / Phytochrome / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / GAF domain / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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Phasing

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

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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

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