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- PDB-5lly: Photosensory Module of Bacteriophytochrome linked Diguanylyl Cycl... -

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Basic information

Entry
Database: PDB / ID: 5lly
TitlePhotosensory Module of Bacteriophytochrome linked Diguanylyl Cyclase from Idiomarina species A28L
ComponentsDiguanylate cyclase (GGDEF) domain-containing protein
KeywordsSIGNALING PROTEIN / bacteriophytochrome / diguanylate cyclase / light-regulation / c-di-GMP / hydrolase
Function / homology
Function and homology information


diguanylate cyclase / detection of visible light / photoreceptor activity / regulation of DNA-templated transcription / GTP binding / metal ion binding
Similarity search - Function
: / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / Diguanylate cyclase, GGDEF domain / PAS fold / Phytochrome, central region / Phytochrome region / diguanylate cyclase / GAF domain ...: / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / Diguanylate cyclase, GGDEF domain / PAS fold / Phytochrome, central region / Phytochrome region / diguanylate cyclase / 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: 2.4 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
Revision 1.2Aug 16, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 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_conn
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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)243,35418
Polymers240,5444
Non-polymers2,81014
Water6,377354
1
D: Diguanylate cyclase (GGDEF) domain-containing protein
C: Diguanylate cyclase (GGDEF) domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,6779
Polymers120,2722
Non-polymers1,4057
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-75 kcal/mol
Surface area44780 Å2
MethodPISA
2
A: Diguanylate cyclase (GGDEF) domain-containing protein
B: Diguanylate cyclase (GGDEF) domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,6779
Polymers120,2722
Non-polymers1,4057
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-79 kcal/mol
Surface area45130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.500, 129.000, 122.010
Angle α, β, γ (deg.)90.000, 96.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 60135.895 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Idiomarina sp. A28L (bacteria) / Gene: A28LD_0430 / 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.: 4 / Source method: obtained synthetically / Formula: C33H37N4O6
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O
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: 2.72 Å3/Da / Density % sol: 54.7 %
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: MASSIF-3 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 17, 2016
RadiationMonochromator: lN2-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.4→48.15 Å / Num. obs: 93405 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 2.85 % / Biso Wilson estimate: 48.82 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.31
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.4-2.50.651.470.627194.1
2.5-2.60.51.990.744194.3
2.6-2.70.3692.760.847195.1
2.7-2.80.2733.720.914195.2
2.8-2.90.2154.660.942195.3
2.9-30.1695.820.957194.2
3-3.10.1427.120.97194.6
3.1-3.50.09511.130.989193.6
3.5-40.05817.270.994191.8
4-60.0423.250.996189.6
6-100.03225.160.998188.8
10-200.02631.580.998188.8
200.02531.230.998177

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.22 Å48.13 Å
Translation7.22 Å48.13 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LLW

5llw


Resolution: 2.4→48.133 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / Phase error: 25.47
RfactorNum. reflection% reflection
Rfree0.2303 4668 5 %
Rwork0.1774 --
obs0.18 93304 93.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.21 Å2 / Biso mean: 58.7025 Å2 / Biso min: 25.11 Å2
Refinement stepCycle: final / Resolution: 2.4→48.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16237 0 192 354 16783
Biso mean--48.03 48.57 -
Num. residues----2013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816871
X-RAY DIFFRACTIONf_angle_d0.89122943
X-RAY DIFFRACTIONf_chiral_restr0.0512508
X-RAY DIFFRACTIONf_plane_restr0.0062966
X-RAY DIFFRACTIONf_dihedral_angle_d11.94510095
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.42730.34711560.2962967312394
2.4273-2.45580.32891560.28852958311493
2.4558-2.48580.34281590.27452993315294
2.4858-2.51720.32151550.26362930308594
2.5172-2.55040.32461590.26033013317295
2.5504-2.58530.27961580.2573005316395
2.5853-2.62220.32871580.23692985314395
2.6222-2.66140.29341570.23522997315495
2.6614-2.70290.29441600.24333033319395
2.7029-2.74730.28561600.22123043320396
2.7473-2.79460.27221580.22033016317495
2.7946-2.84540.26821590.2113017317696
2.8454-2.90020.26341580.21553005316395
2.9002-2.95930.31951580.21342978313694
2.9593-3.02370.31341570.21982991314894
3.0237-3.0940.29961570.21132994315194
3.094-3.17140.25051580.19973007316594
3.1714-3.25710.27621560.19132953310994
3.2571-3.35290.26291580.19212987314593
3.3529-3.46110.24211540.18362942309693
3.4611-3.58480.21441540.17652958311293
3.5848-3.72830.23551490.17252878302791
3.7283-3.89790.22621560.1652951310792
3.8979-4.10330.19391500.1482855300590
4.1033-4.36020.18991510.13652834298589
4.3602-4.69660.17131510.12392874302590
4.6966-5.16870.18041510.13432863301490
5.1687-5.91550.17941530.15232891304490
5.9155-7.44850.19481500.16982834298489
7.4485-48.14260.1811520.14482884303688
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)
12.2183-0.21960.25991.8934-0.47231.8394-0.0393-0.0062-0.2066-0.25890.09110.02730.4491-0.3776-0.00180.6775-0.10390.02090.3631-0.04690.3305-17.5425-27.898220.5265
21.03350.1777-0.16871.6632-0.12912.4123-0.0790.0221-0.01560.1129-0.0528-0.0906-0.0180.2490.12770.3987-0.0472-0.02720.2842-0.00110.2831-3.3212-13.425113.2063
30.1647-0.2383-0.00080.00650.12393.0942-0.04980.1849-0.13430.0015-0.1555-0.2433-0.64851.21620.16040.6521-0.2925-0.01720.88540.06270.595612.8271-4.7476-15.9144
41.739-0.887-0.2313.7312-0.41441.9014-0.2671-0.43210.39030.42510.35750.1924-0.5762-0.2817-0.04680.6260.17070.02460.5227-0.04840.5436-34.014414.968212.834
51.301-0.6489-0.60062.15940.26942.6452-0.04980.0440.0918-0.25380.08810.225-0.1323-0.548-0.02780.3684-0.0042-0.07860.33690.00450.3841-33.11622.2151-4.7465
60.9854-0.324-0.39170.56510.45212.72260.02880.2370.1832-0.20270.0417-0.0322-0.270.2915-0.06930.5221-0.1141-0.07060.27310.06040.3764-12.4366-2.5563-33.5112
74.70981.33610.06652.53810.33492.696-0.11290.9548-0.4388-0.2386-0.00530.16980.3472-0.3720.05950.488-0.002-0.08050.6337-0.12480.5981-41.4069-33.2688-73.8659
82.5080.54860.30181.14330.11652.1602-0.09740.09890.06810.0397-0.03530.3677-0.2151-0.36530.1420.31050.02880.02840.2847-0.01790.4317-36.3167-22.3438-55.5778
91.2103-0.23840.50810.79820.18832.8948-0.0373-0.2378-0.08230.37680.0320.16020.4398-0.0731-0.08170.5387-0.04770.08180.2132-0.01380.4328-22.8914-29.0513-23.2495
103.68991.1004-1.21442.6997-0.85232.42770.0648-0.21720.20790.18970.02180.01-0.566-0.0776-0.030.5996-0.0066-0.02130.3932-0.0130.2992-2.4535-9.6684-76.2326
111.79131.1102-0.54852.655-0.74582.3327-0.1259-0.0202-0.1061-0.1580.0237-0.17920.14460.22710.1090.36520.01890.00010.36450.00220.3058-0.7264-30.4591-66.04
120.3075-0.09420.27960.8403-1.19852.8657-0.0658-0.0463-0.06070.15490.033-0.1239-0.00020.19970.05270.5770.0441-0.00350.3809-0.01370.44780.9974-45.1582-34.3149
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 9 through 127 )B9 - 127
2X-RAY DIFFRACTION2chain 'B' and (resid 128 through 290 )B128 - 290
3X-RAY DIFFRACTION3chain 'B' and (resid 291 through 515 )B291 - 515
4X-RAY DIFFRACTION4chain 'A' and (resid 9 through 127 )A9 - 127
5X-RAY DIFFRACTION5chain 'A' and (resid 128 through 290 )A128 - 290
6X-RAY DIFFRACTION6chain 'A' and (resid 291 through 522 )A291 - 522
7X-RAY DIFFRACTION7chain 'C' and (resid 10 through 127 )C10 - 127
8X-RAY DIFFRACTION8chain 'C' and (resid 128 through 290 )C128 - 290
9X-RAY DIFFRACTION9chain 'C' and (resid 291 through 522 )C291 - 522
10X-RAY DIFFRACTION10chain 'D' and (resid 16 through 127 )D16 - 127
11X-RAY DIFFRACTION11chain 'D' and (resid 128 through 290 )D128 - 290
12X-RAY DIFFRACTION12chain 'D' and (resid 291 through 517 )D291 - 517

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