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

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Basic information

Entry
Database: PDB / ID: 5llx
TitleBacteriophytochrome activated diguanylyl cyclase from Idiomarina species A28L with GTP bound
ComponentsDiguanylate cyclase (GGDEF) domain-containing protein
KeywordsTRANSFERASE / bacteriophytochrome / diguanylate cyclase / light-regulation / GTP / soak
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 / Phytochrome chromophore attachment domain ...: / Phytochrome / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / PAS domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / Reverse transcriptase/Diguanylate cyclase domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Chem-LBV / diguanylate cyclase
Similarity search - Component
Biological speciesIdiomarina sp. A28L (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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 1.2May 1, 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 / 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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 1.3Oct 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
A: Diguanylate cyclase (GGDEF) domain-containing protein
B: Diguanylate cyclase (GGDEF) domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,65810
Polymers156,3212
Non-polymers2,3378
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12670 Å2
ΔGint-81 kcal/mol
Surface area60040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.730, 78.640, 452.040
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 321:327)
21(chain B and resseq 321:327)
12(chain A and resseq 530:682)
22(chain B and resseq 530:682)
13(chain A and resseq 487:525)
23(chain B and resseq 487:525)
14(chain A and resseq 150:206)
24(chain B and resseq 150:206)
15(chain A and resseq 22:120)
25(chain B and resseq 22:120)
16(chain A and resseq 121:149)
26(chain B and resseq 121:149)
17(chain A and resseq 15:21)
27(chain B and resseq 15:21)
18(chain A and (resseq 354:387 or resseq 394:423 or resseq 433:484))
28(chain B and (resseq 354:387 or resseq 394:423 or resseq 433:484))
19(chain A and resseq 338:353)
29(chain B and resseq 338:353)
110(chain A and resseq 207:309)
210(chain B and resseq 207:309)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALARGARG(chain A and resseq 321:327)AA321 - 327323 - 329
211VALVALARGARG(chain B and resseq 321:327)BB321 - 327323 - 329
112ASPASPSERSER(chain A and resseq 530:682)AA530 - 682532 - 684
212ASPASPSERSER(chain B and resseq 530:682)BB530 - 682532 - 684
113ALAALALEULEU(chain A and resseq 487:525)AA487 - 525489 - 527
213ALAALALEULEU(chain B and resseq 487:525)BB487 - 525489 - 527
114ASNASNALAALA(chain A and resseq 150:206)AA150 - 206152 - 208
214ASNASNALAALA(chain B and resseq 150:206)BB150 - 206152 - 208
115ILEILETYRTYR(chain A and resseq 22:120)AA22 - 12024 - 122
215ILEILETYRTYR(chain B and resseq 22:120)BB22 - 12024 - 122
116HISHISILEILE(chain A and resseq 121:149)AA121 - 149123 - 151
216HISHISILEILE(chain B and resseq 121:149)BB121 - 149123 - 151
117ALAALAPROPRO(chain A and resseq 15:21)AA15 - 2117 - 23
217ALAALAPROPRO(chain B and resseq 15:21)BB15 - 2117 - 23
118LEULEULEULEU(chain A and (resseq 354:387 or resseq 394:423 or resseq 433:484))AA354 - 387356 - 389
128SERSERPROPRO(chain A and (resseq 354:387 or resseq 394:423 or resseq 433:484))AA394 - 423396 - 425
138TYRTYRTRPTRP(chain A and (resseq 354:387 or resseq 394:423 or resseq 433:484))AA433 - 484435 - 486
218LEULEULEULEU(chain B and (resseq 354:387 or resseq 394:423 or resseq 433:484))BB354 - 387356 - 389
228SERSERPROPRO(chain B and (resseq 354:387 or resseq 394:423 or resseq 433:484))BB394 - 423396 - 425
238TYRTYRTRPTRP(chain B and (resseq 354:387 or resseq 394:423 or resseq 433:484))BB433 - 484435 - 486
119HISHISLYSLYS(chain A and resseq 338:353)AA338 - 353340 - 355
219HISHISLYSLYS(chain B and resseq 338:353)BB338 - 353340 - 355
1110METMETTRPTRP(chain A and resseq 207:309)AA207 - 309209 - 311
2110METMETTRPTRP(chain B and resseq 207:309)BB207 - 309209 - 311

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 78160.281 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, diguanylate cyclase

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Non-polymers , 5 types, 12 molecules

#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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.88 Å3/Da / Density % sol: 57.35 %
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. Soaked 5 minutes in GTP 10mM in reservoir solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2016
RadiationMonochromator: chanel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.8→48.0783 Å / Num. obs: 44894 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 4.37 % / Biso Wilson estimate: 78.22 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.184 / Net I/σ(I): 7.81
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.8-2.92.5560.610.142199.3
2.9-31.9180.820.262198.5
3-3.11.4261.160.364198.9
3.1-3.30.9431.780.608197.9
3.3-3.50.5583.160.845198.9
3.5-3.80.3494.970.93197.3
3.8-40.2087.610.968195.9
4-4.30.14110.990.988197.3
4.3-4.50.09914.380.991198.5
4.5-50.08616.060.994195.9
5-60.09115.210.993196.6
6-100.05322.130.998195.2
10-200.02935.030.999193.1
200.02535.340.999186

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.58 Å48.08 Å
Translation7.58 Å48.08 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PadC

Resolution: 2.8→48.078 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.21
RfactorNum. reflection% reflection
Rfree0.2703 2243 5 %
Rwork0.2231 --
obs0.2255 44889 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 183.32 Å2 / Biso mean: 92.4639 Å2 / Biso min: 30.43 Å2
Refinement stepCycle: final / Resolution: 2.8→48.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10647 0 154 4 10805
Biso mean--80.2 56.04 -
Num. residues----1321
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911049
X-RAY DIFFRACTIONf_angle_d0.79714988
X-RAY DIFFRACTIONf_chiral_restr0.0491623
X-RAY DIFFRACTIONf_plane_restr0.0051938
X-RAY DIFFRACTIONf_dihedral_angle_d11.4776596
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A56X-RAY DIFFRACTION5.752TORSIONAL
12B56X-RAY DIFFRACTION5.752TORSIONAL
21A1509X-RAY DIFFRACTION5.752TORSIONAL
22B1509X-RAY DIFFRACTION5.752TORSIONAL
31A364X-RAY DIFFRACTION5.752TORSIONAL
32B364X-RAY DIFFRACTION5.752TORSIONAL
41A558X-RAY DIFFRACTION5.752TORSIONAL
42B558X-RAY DIFFRACTION5.752TORSIONAL
51A944X-RAY DIFFRACTION5.752TORSIONAL
52B944X-RAY DIFFRACTION5.752TORSIONAL
61A274X-RAY DIFFRACTION5.752TORSIONAL
62B274X-RAY DIFFRACTION5.752TORSIONAL
71A60X-RAY DIFFRACTION5.752TORSIONAL
72B60X-RAY DIFFRACTION5.752TORSIONAL
81A1084X-RAY DIFFRACTION5.752TORSIONAL
82B1084X-RAY DIFFRACTION5.752TORSIONAL
91A144X-RAY DIFFRACTION5.752TORSIONAL
92B144X-RAY DIFFRACTION5.752TORSIONAL
101A1002X-RAY DIFFRACTION5.752TORSIONAL
102B1002X-RAY DIFFRACTION5.752TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8001-2.8610.42051380.37242616275499
2.861-2.92760.4221410.375626882829100
2.9276-3.00080.44711390.3642645278498
3.0008-3.08190.34921370.35132606274399
3.0819-3.17260.37441410.34682669281097
3.1726-3.27490.38951380.30972629276799
3.2749-3.3920.40781420.2762689283199
3.392-3.52770.32011390.249826382777100
3.5277-3.68820.30321390.24052650278997
3.6882-3.88260.27121410.23052674281597
3.8826-4.12570.24551370.18942601273896
4.1257-4.44410.21111410.17572677281898
4.4441-4.89090.22981400.16592662280297
4.8909-5.59770.23181410.18182675281696
5.5977-7.04890.24061420.21582716285897
7.0489-48.08540.21661470.19152811295894
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)
12.71631.0998-0.71731.02150.17512.6504-0.33190.1423-0.3501-0.58060.1162-0.304-0.1330.24170.12881.0676-0.00270.00270.40130.05460.619311.81557.0126455.4745
21.00020.49910.47482.66960.36731.8422-0.0198-0.1973-0.06520.1522-0.0339-0.0574-0.0678-0.27530.08571.19370.02120.02920.41840.07010.5517-1.6939.1595472.0675
31.21330.16820.5492-0.0043-0.0092.7346-0.0479-0.6692-0.2944-0.1008-0.09330.06150.3163-0.49580.07850.98840.00340.01460.80280.21820.6995-3.08760.3962504.6895
49.04150.7053-0.6415.7426-0.10785.90710.2457-1.23420.21970.8712-0.09720.3521-0.48460.0078-0.09990.48810.0420.01460.7657-0.05760.729613.84161.9528578.9929
52.7542-1.17810.03081.8148-1.15561.03690.09340.07370.3067-0.1917-0.00140.0088-0.3631-0.2169-0.05861.2076-0.07350.04640.42290.10290.66089.825549.6249474.5022
62.1542-1.31340.21792.9293-0.59611.5016-0.0485-0.19630.2380.4446-0.0197-0.50560.1350.1360.08231.2524-0.081-0.08540.44210.07020.678923.389835.3359484.3001
70.3014-0.0039-0.07653.204-2.93163.52770.0418-0.4130.03930.3959-0.1319-0.2516-0.32760.17440.04520.8239-0.0098-0.05630.77690.05410.617124.115415.3493513.3896
88.01352.79211.15277.38772.68164.37740.6253-0.9647-0.4821.0069-0.5647-0.35350.7542-0.17870.0630.6051-0.0464-0.13370.72420.18920.716711.8715-24.04575.3012
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 521 )B291 - 521
4X-RAY DIFFRACTION4chain 'B' and (resid 530 through 682 )B530 - 682
5X-RAY DIFFRACTION5chain 'A' and (resid 10 through 127 )A10 - 127
6X-RAY DIFFRACTION6chain 'A' and (resid 128 through 290 )A128 - 290
7X-RAY DIFFRACTION7chain 'A' and (resid 291 through 523 )A291 - 523
8X-RAY DIFFRACTION8chain 'A' and (resid 530 through 682 )A530 - 682

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