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- PDB-8c05: LOV-activated diguanylate cyclase, dark-state structure -

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Basic information

Entry
Database: PDB / ID: 8c05
TitleLOV-activated diguanylate cyclase, dark-state structure
ComponentsSensor domain-containing diguanylate cyclase
KeywordsFLAVOPROTEIN / LOV / GGDEF / c-di-GMP / FMN / linker
Function / homology
Function and homology information


diguanylate cyclase / negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase activity / cell adhesion involved in single-species biofilm formation / nucleotide binding / metal ion binding / plasma membrane
Similarity search - Function
: / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS domain / PAS-associated, C-terminal / PAC domain profile. / Nucleotide cyclase / PAC motif ...: / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS domain / PAS-associated, C-terminal / PAC domain profile. / Nucleotide cyclase / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / Reverse transcriptase/Diguanylate cyclase domain / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHATE / FLAVIN MONONUCLEOTIDE / diguanylate cyclase
Similarity search - Component
Biological speciesMethylotenera sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsVide, U. / Winkler, A.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundP34387 Austria
Austrian Science FundDOC 130 doc.funds Austria
CitationJournal: Sci Adv / Year: 2023
Title: Illuminating the inner workings of a natural protein switch: Blue-light sensing in LOV-activated diguanylate cyclases.
Authors: Vide, U. / Kasapovic, D. / Fuchs, M. / Heimbock, M.P. / Totaro, M.G. / Zenzmaier, E. / Winkler, A.
History
DepositionDec 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor domain-containing diguanylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8974
Polymers36,2421
Non-polymers6553
Water00
1
A: Sensor domain-containing diguanylate cyclase
hetero molecules

A: Sensor domain-containing diguanylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7938
Polymers72,4842
Non-polymers1,3096
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)56.350, 56.350, 318.040
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Sensor domain-containing diguanylate cyclase


Mass: 36242.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylotenera sp. (bacteria) / Gene: CTY33_01890 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S5LZS0
#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-DPO / DIPHOSPHATE


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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: 2.02 Å3/Da / Density % sol: 39.1 % / Description: bipyramid-like crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Sodium formate, 0.1 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate, 0.1 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium oxamate, 0.1 M Sodium HEPES; MOPS (acid), pH ...Details: 0.1 M Sodium formate, 0.1 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate, 0.1 M Potassium sodium tartrate tetrahydrate, 0.1 M Sodium oxamate, 0.1 M Sodium HEPES; MOPS (acid), pH 7.5, 20% v/v Glycerol; 10% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03312 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2021
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03312 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 11310 / % possible obs: 99.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 80.05 Å2 / CC1/2: 1 / Rrim(I) all: 0.06 / Net I/σ(I): 27.21
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 5.36 % / Mean I/σ(I) obs: 4.39 / Num. unique obs: 1202 / CC1/2: 0.993 / Rrim(I) all: 0.82 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487model building
PHENIX1.20.1_4487refinement
XDS1.02data reduction
XSCALEVERSION Feb 5, 2021 BUILT=20210323data scaling
PHASER1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.8 Å / SU ML: 0.3039 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.1624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2978 558 5 %
Rwork0.2547 10595 -
obs0.2569 11153 98.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 114.09 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2433 0 41 0 2474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00152518
X-RAY DIFFRACTIONf_angle_d0.39333416
X-RAY DIFFRACTIONf_chiral_restr0.0382385
X-RAY DIFFRACTIONf_plane_restr0.0023435
X-RAY DIFFRACTIONf_dihedral_angle_d10.0939927
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.750.41781330.3182501X-RAY DIFFRACTION97.09
2.75-3.150.38311340.34112572X-RAY DIFFRACTION97.87
3.15-3.970.36111390.29372634X-RAY DIFFRACTION99.14
3.97-48.80.24961520.22312888X-RAY DIFFRACTION99.77
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)
15.03428848330.8914728929564.394096765797.984156437772.469973877865.922351196721.37394000609-0.597904766312-2.316761317661.48316477511-0.630513684717-2.777000224572.582325896450.818262642459-0.2820095230411.968873712670.663746937992-0.009250321555681.400108415210.1538907531311.080332761821.5636785399-3.731202026133.58278469184
23.78846191886-0.3563819424850.3546897233123.691798695140.7260551190231.97054867913-0.3818374628160.300602893688-0.0273295664491-0.332819928080.3161176139660.07272713353860.6999299335650.1569151315190.02267648323961.56881214498-0.1083394686840.07824260553010.543792395715-0.01058136609260.8193530862879.94091460494-6.05570979632-13.6689804265
32.49265326513-0.09436715447612.626633925860.142213202941-0.06861541037513.034882708780.987170050314-2.038074297851.347857106971.10785922969-0.3539293578730.9644776565370.6831470038940.253826736101-0.7437007210021.709911911480.08432894436350.2341818860222.52839399428-0.6687852509391.5354504455228.34287100394.51104842391-15.3336548756
42.55852312331-1.824584181780.6011845193833.29467643153-0.2517092805683.079591685570.0136053328615-0.487969202393-0.5437252831730.2099567999790.1478960987310.821806291234-0.505577878682-0.275120369028-0.1969124237451.44474166991-0.0279333471650.1274336473310.4681057920110.01831357621120.893615957609-5.307328372866.90156759955-2.71394273703
53.687683509711.16089949170.9324947640481.609782022770.3409223428911.84203678878-0.4027784609150.411430476259-0.003207878000390.07622715083430.21408063840.147123025557-0.663107517646-0.2143450486970.187817788981.67129969043-0.383727874427-0.0865342265290.3277518645930.1003046362260.893750061568-1.8675806405116.9975792723-16.3198612428
63.98292748707-1.238175219530.001833369786654.970451184990.07898985108583.07568434513-0.5377262970670.4247147242230.8566863491170.7603228430020.522925695092-0.106517705516-0.6891428901590.7507311613160.1624175275961.67583608556-0.40381656774-0.2678899612060.3786705147710.2106575709921.052301593945.0182246088125.1985510769-16.2165751673
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 14 )A4 - 141 - 11
22chain 'A' and (resid 15 through 103 )A15 - 10312 - 100
33chain 'A' and (resid 104 through 110 )A104 - 110101 - 107
44chain 'A' and (resid 111 through 161 )A111 - 161108 - 154
55chain 'A' and (resid 162 through 275 )A162 - 275155 - 268
66chain 'A' and (resid 276 through 402 )A - C276 - 402269

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