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- PDB-5llw: Bacteriophytochrome activated diguanylyl cyclase from Idiomarina ... -

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Basic information

Entry
Database: PDB / ID: 5llw
TitleBacteriophytochrome activated diguanylyl cyclase from Idiomarina species A28L
ComponentsDiguanylate cyclase (GGDEF) domain-containing protein
KeywordsTRANSFERASE / bacteriophytochrome / diguanylate cyclase / light-regulation / c-di-GMP / GTP / hydrolase
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. / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Chem-LBV / diguanylate cyclase
Similarity search - Component
Biological speciesIdiomarina sp. A28L (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 3 Å
AuthorsGourinchas, G. / Winkler, A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP27124 Austria
CitationJournal: Sci Adv / Year: 2017
Title: Long-range allosteric signaling in red light-regulated diguanylyl cyclases.
Authors: Gourinchas, G. / Etzl, S. / Gobl, C. / Vide, U. / Madl, T. / Winkler, A.
History
DepositionJul 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references

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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)159,1576
Polymers157,9152
Non-polymers1,2424
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9920 Å2
ΔGint-62 kcal/mol
Surface area62520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.870, 77.800, 439.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 124:189 or resseq 191:206 or resseq 208:309))
21(chain B and (resseq 124:189 or resseq 191:206 or resseq 208:309))
12(chain A and resseq 8:120)
22(chain B and resseq 8:120)
13(chain A and resseq 530:683)
23(chain B and resseq 530:683)
14(chain A and (resseq 321:334 or resseq 336:389 or resseq 393:425 or resseq 432:525))
24(chain B and (resseq 321:335 or resseq 337:389 or resseq 393:425 or resseq 432:525))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 124:189 or resseq 191:206 or resseq 208:309))A124 - 189
121(chain A and (resseq 124:189 or resseq 191:206 or resseq 208:309))A191 - 206
131(chain A and (resseq 124:189 or resseq 191:206 or resseq 208:309))A208 - 309
211(chain B and (resseq 124:189 or resseq 191:206 or resseq 208:309))B124 - 189
221(chain B and (resseq 124:189 or resseq 191:206 or resseq 208:309))B191 - 206
231(chain B and (resseq 124:189 or resseq 191:206 or resseq 208:309))B208 - 309
112(chain A and resseq 8:120)A8 - 120
212(chain B and resseq 8:120)B8 - 120
113(chain A and resseq 530:683)A530 - 683
213(chain B and resseq 530:683)B530 - 683
114(chain A and (resseq 321:334 or resseq 336:389 or resseq 393:425 or resseq 432:525))A321 - 334
124(chain A and (resseq 321:334 or resseq 336:389 or resseq 393:425 or resseq 432:525))A336 - 389
134(chain A and (resseq 321:334 or resseq 336:389 or resseq 393:425 or resseq 432:525))A393 - 425
144(chain A and (resseq 321:334 or resseq 336:389 or resseq 393:425 or resseq 432:525))A432 - 525
214(chain B and (resseq 321:335 or resseq 337:389 or resseq 393:425 or resseq 432:525))B321 - 335
224(chain B and (resseq 321:335 or resseq 337:389 or resseq 393:425 or resseq 432:525))B337 - 389
234(chain B and (resseq 321:335 or resseq 337:389 or resseq 393:425 or resseq 432:525))B393 - 425
244(chain B and (resseq 321:335 or resseq 337:389 or resseq 393:425 or resseq 432:525))B432 - 525

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Diguanylate cyclase (GGDEF) domain-containing protein / Photosensory Module of Bacteriophytochrome


Mass: 78957.516 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
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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: 2.78 Å3/Da / Density % sol: 55.83 %
Description: Plate-like elongated crystals appeared after overnight incubation under dark conditions and reached final dimensions within 5 days.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 0.1 M ammonium acetate, 17% (w/v) PEG 10,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979168 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2015
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979168 Å / Relative weight: 1
ReflectionResolution: 2.8→68.7 Å / Num. obs: 67335 / % possible obs: 81.1 % / Observed criterion σ(I): -3 / Redundancy: 14.94 % / Biso Wilson estimate: 91.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.132 / Net I/σ(I): 15.85
Reflection shell
Resolution (Å)Highest resolution (Å)Diffraction-IDRmerge(I) obsMean I/σ(I) obsCC1/2% possible all
2.8-2.91
2.9-31
3-3.111.6240.830.29698.8
3.1-3.510.7352.430.82699.7
3.5-410.27112.610.991100
4-610.13225.920.997100
6-1010.08135.750.999100
10-2010.06245.340.999100
2010.05447.640.99996.1

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
SOLVEphasing
RESOLVEphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 3→63.518 Å / SU ML: 0.62 / Cross valid method: FREE R-VALUE / Phase error: 30.09
RfactorNum. reflection% reflection
Rfree0.2587 3082 4.58 %
Rwork0.2047 --
obs0.2072 67329 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 193.74 Å2 / Biso mean: 97.785 Å2 / Biso min: 47.14 Å2
Refinement stepCycle: final / Resolution: 3→63.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10840 0 88 0 10928
Biso mean--73.92 --
Num. residues----1345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111178
X-RAY DIFFRACTIONf_angle_d1.12115152
X-RAY DIFFRACTIONf_chiral_restr0.0661645
X-RAY DIFFRACTIONf_plane_restr0.0081975
X-RAY DIFFRACTIONf_dihedral_angle_d11.2546728
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1717X-RAY DIFFRACTION5.818TORSIONAL
12B1717X-RAY DIFFRACTION5.818TORSIONAL
21A1036X-RAY DIFFRACTION5.818TORSIONAL
22B1036X-RAY DIFFRACTION5.818TORSIONAL
31A1324X-RAY DIFFRACTION5.818TORSIONAL
32B1324X-RAY DIFFRACTION5.818TORSIONAL
41A1737X-RAY DIFFRACTION5.818TORSIONAL
42B1737X-RAY DIFFRACTION5.818TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0001-3.0470.48241290.48362789291898
3.047-3.09690.43781460.44762941308799
3.0969-3.15030.43851420.4242901304399
3.1503-3.20760.50331530.37562964311799
3.2076-3.26930.36691330.328728402973100
3.2693-3.3360.30041310.287729463077100
3.336-3.40860.32421480.259829823130100
3.4086-3.48790.33111350.268728562991100
3.4879-3.57510.28861460.246430013147100
3.5751-3.67170.32591500.248128713021100
3.6717-3.77980.31291340.203228963030100
3.7798-3.90170.2111230.192630513174100
3.9017-4.04120.23431480.176128633011100
4.0412-4.2030.19971410.169629413082100
4.203-4.39420.2461380.158629083046100
4.3942-4.62580.22811420.151330113153100
4.6258-4.91550.19361490.159928492998100
4.9155-5.29490.23311370.166128973034100
5.2949-5.82740.26791460.179629673113100
5.8274-6.66980.23481350.194529103045100
6.6698-8.40020.22981350.187129513086100
8.4002-63.53170.22191410.181529123053100
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)
13.32120.8330.74732.6074-0.36432.5806-0.24970.08030.3416-0.5160.16490.6238-0.0548-0.33140.00010.9929-0.0137-0.02120.7072-0.05890.790110.2532.1854443.2662
21.52190.6555-0.40493.00960.26082.9674-0.1359-0.10640.05840.0454-0.0683-0.04860.09630.335400.89650.09480.06290.6365-0.08050.666123.877130.364459.7506
30.2375-0.2789-1.04160.13690.81843.7603-0.0618-0.56570.29770.0583-0.08560.0078-0.31160.7776-0.00020.8979-0.0571-0.01271.1991-0.19480.997724.295540.3835494.5056
43.35591.79991.18384.27941.31233.97780.1917-0.6791-0.06980.533-0.0855-0.12010.0972-0.13820.00010.7043-0.0042-0.03751.35350.05670.85369.89941.9608565.4736
54.0551-0.78710.37784.079-0.67452.66770.01380.0557-0.2002-0.11880.1298-0.06060.39480.00560.00021.0367-0.0855-0.00210.5398-0.13760.850511.8338-9.9038463.2908
61.6491-0.8533-0.2283.49241.31562.38190.0051-0.2489-0.24220.1249-0.150.45770.0406-0.32050.00041.0177-0.04260.14160.6568-0.10560.8992-1.15174.1868472.4727
70.1831-0.07050.25632.43352.49973.085-0.0798-0.4305-0.13020.7142-0.10270.30230.5391-0.0970.00071.04430.02130.18781.123-0.16620.9914-1.765625.5064501.8156
84.12741.2561.21525.6242-1.00475.09950.1798-0.76090.12340.5118-0.29690.5694-0.1439-0.1601-0.00170.6488-0.0630.07411.4285-0.11690.845614.906469.4072558.7327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 8 through 127 )B8 - 127
2X-RAY DIFFRACTION2chain 'B' and (resid 128 through 290 )B128 - 290
3X-RAY DIFFRACTION3chain 'B' and (resid 291 through 527 )B291 - 527
4X-RAY DIFFRACTION4chain 'B' and (resid 528 through 683 )B528 - 683
5X-RAY DIFFRACTION5chain 'A' and (resid 8 through 127 )A8 - 127
6X-RAY DIFFRACTION6chain 'A' and (resid 128 through 290 )A128 - 290
7X-RAY DIFFRACTION7chain 'A' and (resid 291 through 527 )A291 - 527
8X-RAY DIFFRACTION8chain 'A' and (resid 528 through 683 )A528 - 683

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