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

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Basic information

Entry
Database: PDB / ID: 6sax
TitleChromophore binding domain of bacteriophytochrome linked diguanylyl cyclase from Idiomarina species A28L (Pr-state monomer).
ComponentsDiguanylate cyclase (GGDEF) domain-containing protein
KeywordsFLUORESCENT PROTEIN / bacteriophytochrome / biliverdin / monomer / protein
Function / homology
Function and homology information


diguanylate cyclase / detection of visible light / photoreceptor activity / GTP binding / regulation of DNA-templated transcription / metal ion binding
Similarity search - Function
Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. ...Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / 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: 2.4 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Diguanylate cyclase (GGDEF) domain-containing protein
A: Diguanylate cyclase (GGDEF) domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9714
Polymers71,8002
Non-polymers1,1712
Water1,982110
1
B: Diguanylate cyclase (GGDEF) domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4852
Polymers35,9001
Non-polymers5861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Diguanylate cyclase (GGDEF) domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4852
Polymers35,9001
Non-polymers5861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.960, 149.960, 77.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 35899.766 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C33H37N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.52 Å3/Da / Density % sol: 65.01 % / Description: long plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.24 M sodium malonate pH 7.0, 20 % PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 2.4→53.894 Å / Num. obs: 38887 / % possible obs: 99.7 % / Redundancy: 10.159 % / Biso Wilson estimate: 48.198 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.202 / Rrim(I) all: 0.213 / Χ2: 0.95 / Net I/σ(I): 9.69 / Num. measured all: 395067 / Scaling rejects: 20
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
2.4-2.510.4181.6181.5746393447744530.5591.70299.5
2.5-2.810.3471.0192.55102020989698600.7761.07299.6
2.8-310.2030.5914.2646474457045550.9140.62299.7
3-3.410.2150.3147.4663320622161990.9770.3399.6
3.4-3.710.3230.16813.0131641307030650.9910.17799.8
3.7-410.1930.13215.8122730223222300.9940.13999.9
4-69.5850.0921.3457302598159780.9970.09599.9
6-1010.0870.06827.8720084199419910.9980.07299.8
10-209.3980.0537.9146334984930.9980.05399
20-53.8947.460.04734.7147078630.9960.05280.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.35 Å53.89 Å
Translation4.35 Å53.89 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: 5llw

5llw


Resolution: 2.4→53.894 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.35
RfactorNum. reflection% reflection
Rfree0.2359 1945 5 %
Rwork0.1976 --
obs0.1995 38885 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.36 Å2 / Biso mean: 48.8571 Å2 / Biso min: 23.15 Å2
Refinement stepCycle: final / Resolution: 2.4→53.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4964 0 86 110 5160
Biso mean--38.67 41.6 -
Num. residues----612
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4001-2.46010.33121380.29532626100
2.4601-2.52660.34031370.28322609100
2.5266-2.60090.3311390.28232636100
2.6009-2.68490.28561380.25992608100
2.6849-2.78080.27771370.24112611100
2.7808-2.89220.27771390.2352636100
2.8922-3.02380.25551380.23592634100
3.0238-3.18320.29031390.2393263799
3.1832-3.38260.31331380.20932625100
3.3826-3.64370.23121390.19392642100
3.6437-4.01030.211400.19012643100
4.0103-4.59030.19271400.15172662100
4.5903-5.78230.18681400.16062661100
5.7823-53.8940.18631430.1568271099

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