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Basic information

Entry
Database: PDB / ID: 6et7
TitleActivated heterodimer of the bacteriophytochrome regulated diguanylyl cyclase variant - S505V A526V - from Idiomarina species A28L
ComponentsDiguanylate cyclase (GGDEF) domain-containing protein
KeywordsTRANSFERASE / red light / phytochrome / GGDEF / asymmetry
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 / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain ...: / Phytochrome / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / 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
Chem-LBV / diguanylate cyclase
Similarity search - Component
Biological speciesIdiomarina sp. A28L (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.852 Å
AuthorsGourinchas, G. / Winkler, A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP27124 Austria
CitationJournal: Elife / Year: 2018
Title: Asymmetric activation mechanism of a homodimeric red light regulated photoreceptor.
Authors: Gourinchas, G. / Heintz, U. / Winkler, A.
History
DepositionOct 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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_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_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 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)157,6436
Polymers156,4012
Non-polymers1,2424
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-53 kcal/mol
Surface area61470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.460, 78.420, 443.850
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 11:120)
22(chain B and resseq 11:120)
13(chain A and resseq 530:682)
23(chain B and resseq 530:682)
14(chain A and (resseq 321:334 or resseq 395:408 or resseq 415:424 or resseq 490:527))
24(chain B and (resseq 321:334 or resseq 395:408 or resseq 415:424 or resseq 490:527))

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
111THRTHRSERSER(chain A and (resseq 124:189 or resseq 191:206 or resseq 208:309))AA124 - 189126 - 191
121LEULEUALAALA(chain A and (resseq 124:189 or resseq 191:206 or resseq 208:309))AA191 - 206193 - 208
131TYRTYRTRPTRP(chain A and (resseq 124:189 or resseq 191:206 or resseq 208:309))AA208 - 309210 - 311
211THRTHRSERSER(chain B and (resseq 124:189 or resseq 191:206 or resseq 208:309))BB124 - 189126 - 191
221LEULEUALAALA(chain B and (resseq 124:189 or resseq 191:206 or resseq 208:309))BB191 - 206193 - 208
231TYRTYRTRPTRP(chain B and (resseq 124:189 or resseq 191:206 or resseq 208:309))BB208 - 309210 - 311
112SERSERTYRTYR(chain A and resseq 11:120)AA11 - 12013 - 122
212SERSERTYRTYR(chain B and resseq 11:120)BB11 - 12013 - 122
113ASPASPSERSER(chain A and resseq 530:682)AA530 - 682532 - 684
213ASPASPSERSER(chain B and resseq 530:682)BB530 - 682532 - 684
114VALVALALAALA(chain A and (resseq 321:334 or resseq 395:408 or resseq 415:424 or resseq 490:527))AA321 - 334323 - 336
124LEULEUGLYGLY(chain A and (resseq 321:334 or resseq 395:408 or resseq 415:424 or resseq 490:527))AA395 - 408397 - 410
134ARGARGLEULEU(chain A and (resseq 321:334 or resseq 395:408 or resseq 415:424 or resseq 490:527))AA415 - 424417 - 426
144TYRTYRSERSER(chain A and (resseq 321:334 or resseq 395:408 or resseq 415:424 or resseq 490:527))AA490 - 527492 - 529
214VALVALALAALA(chain B and (resseq 321:334 or resseq 395:408 or resseq 415:424 or resseq 490:527))BB321 - 334323 - 336
224LEULEUGLYGLY(chain B and (resseq 321:334 or resseq 395:408 or resseq 415:424 or resseq 490:527))BB395 - 408397 - 410
234ARGARGLEULEU(chain B and (resseq 321:334 or resseq 395:408 or resseq 415:424 or resseq 490:527))BB415 - 424417 - 426
244TYRTYRSERSER(chain B and (resseq 321:334 or resseq 395:408 or resseq 415:424 or resseq 490:527))BB490 - 527492 - 529

NCS ensembles :
ID
1
2
3
4

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Components

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


Mass: 78200.391 Da / Num. of mol.: 2 / Mutation: S505V, A526V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Idiomarina sp. A28L (bacteria) / Gene: A28LD_0430 / Plasmid: pETM-11 / 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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M magnesium formate, 12 % (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0089 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2017
RadiationMonochromator: Si-111 and Si-113 reflection / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0089 Å / Relative weight: 1
ReflectionResolution: 2.85→49.306 Å / Num. obs: 41744 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.239 % / Biso Wilson estimate: 61.62 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.21 / Rrim(I) all: 0.221 / Χ2: 0.922 / Net I/σ(I): 9.28 / Num. measured all: 427424 / Scaling rejects: 76
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
2.85-2.9510.7661.4911.5543281402740200.5561.56499.8
2.95-310.711.1781.9519750184418440.6581.237100
3-3.210.6110.9042.6265290615461530.7740.95100
3.2-3.310.3720.6553.6627132261726160.8810.69100
3.3-3.59.9790.4555.1542411425142500.9290.48100
3.5-410.2830.2848.1875744737373660.970.29999.9
4-610.110.13415.2210833110716107150.9940.141100
6-109.7580.08220.0235891368336780.9980.08799.9
10-208.9780.05330.1384849469450.9990.05699.9
20-49.3067.070.05728.1911101681570.9970.06193.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation8.31 Å58.76 Å
Translation8.31 Å58.76 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PHASER2.6.0phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LLW, 5LLX

5llw

5llx


Resolution: 2.852→49.306 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2746 2089 5 %
Rwork0.2157 39650 -
obs0.2187 41739 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.45 Å2 / Biso mean: 83.7576 Å2 / Biso min: 6.91 Å2
Refinement stepCycle: final / Resolution: 2.852→49.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10428 0 88 6 10522
Biso mean--58.37 31.26 -
Num. residues----1291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810737
X-RAY DIFFRACTIONf_angle_d1.14114546
X-RAY DIFFRACTIONf_chiral_restr0.0641587
X-RAY DIFFRACTIONf_plane_restr0.0071891
X-RAY DIFFRACTIONf_dihedral_angle_d11.6926454
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1770X-RAY DIFFRACTION8.042TORSIONAL
12B1770X-RAY DIFFRACTION8.042TORSIONAL
21A1045X-RAY DIFFRACTION8.042TORSIONAL
22B1045X-RAY DIFFRACTION8.042TORSIONAL
31A1466X-RAY DIFFRACTION8.042TORSIONAL
32B1466X-RAY DIFFRACTION8.042TORSIONAL
41A682X-RAY DIFFRACTION8.042TORSIONAL
42B682X-RAY DIFFRACTION8.042TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.852-2.91840.37771400.321826612801
2.9184-2.99130.35351350.288725632698
2.9913-3.07220.32921350.252625792714
3.0722-3.16260.31251370.252125932730
3.1626-3.26470.34931370.252425922729
3.2647-3.38130.31551360.245525842720
3.3813-3.51670.29441380.236926342772
3.5167-3.67670.27511360.214225762712
3.6767-3.87040.28551400.214526492789
3.8704-4.11280.25571400.199526512791
4.1128-4.43020.25981390.183526272766
4.4302-4.87560.22581410.173326822823
4.8756-5.58030.24661390.19926592798
5.5803-7.02740.27461440.231527212865
7.0274-49.31350.25491520.204628793031
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)
12.70990.8537-1.07483.3908-0.12611.9103-0.49790.4605-0.2467-0.5480.3645-0.6635-0.02380.57790.01740.55-0.06040.03310.2168-0.05720.669113.36337.2818447.0281
21.44730.59020.16913.77080.57433.2517-0.1005-0.23270.0843-0.04760.01560.0527-0.012-0.33220.02390.28590.0458-0.01180.15550.02470.576-0.70628.8426463.9478
32.45091.4107-0.11531.49561.02541.48260.502-1.2513-0.48260.8691-0.5199-0.06390.8414-0.3610.09420.9311-0.1165-0.07060.86430.17680.6977-3.38890.7801492.355
41.52261.18320.70542.2647-0.16142.70340.0453-0.45110.19240.60980.11960.0739-0.21270.0541-0.11140.9240.1563-0.03731.10280.01780.671115.91271.9298565.1358
52.8989-1.1441-0.59656.96810.67862.058-0.06520.02720.2747-0.3240.1352-0.0962-0.2726-0.1625-0.01770.50020.03140.03530.16920.05950.656711.051349.5395466.2302
62.1013-0.28880.22824.751-0.29151.85140.0178-0.12980.12590.3891-0.0424-0.97850.15780.20790.00530.39580.0246-0.10650.1981-0.01230.782824.063734.9389476.6088
71.2619-0.97440.80412.1817-3.11516.65290.0445-1.01840.01210.94250.1362-0.2336-0.35690.1963-0.12810.97790.0338-0.18960.8863-0.04450.787525.556718.2089504.2772
81.13721.2718-1.19212.8729-1.47832.79610.0588-0.2027-0.2280.3034-0.0097-0.12010.4736-0.2366-0.12930.9830.1084-0.0451.35210.09280.696111.3154-22.3188560.6526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 10 through 127 )B10 - 127
2X-RAY DIFFRACTION2chain 'B' and (resid 128 through 290 )B128 - 290
3X-RAY DIFFRACTION3chain 'B' and (resid 291 through 499 )B291 - 499
4X-RAY DIFFRACTION4chain 'B' and (resid 500 through 682 )B500 - 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 499 )A291 - 499
8X-RAY DIFFRACTION8chain 'A' and (resid 500 through 682 )A500 - 682

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