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- PDB-9jry: Crystal structure of FiDCB, a dual-cysteine cyanobacterial phytoc... -

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Basic information

Entry
Database: PDB / ID: 9jry
TitleCrystal structure of FiDCB, a dual-cysteine cyanobacterial phytochrome of Fischerella sp. PCC 9605
ComponentsFiDCB
KeywordsSIGNALING PROTEIN / Cyanobacteria / Dual-Cysteine Bacteriophytochrome
Function / homologyChem-BLR
Function and homology information
Biological speciesFischerella sp. PCC 9605 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsYang, H.W. / Park, Y.-I. / Song, J.-J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Other governmentKGM1002311
National Research Foundation (NRF, Korea)2020M3A9G710393422 Korea, Republic Of
CitationJournal: Febs J. / Year: 2025
Title: Dual-Cys bacteriophytochromes: intermediates in cyanobacterial phytochrome evolution?
Authors: Yang, H.W. / Song, J.Y. / Song, J.J. / Kim, Y.W. / Rockwell, N.C. / Kim, W. / Kim, H. / Lagarias, J.C. / Park, Y.I.
History
DepositionSep 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FiDCB
B: FiDCB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,3094
Polymers119,1392
Non-polymers1,1692
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-13 kcal/mol
Surface area41660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.551, 147.131, 88.076
Angle α, β, γ (deg.)90.000, 99.145, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein FiDCB


Mass: 59569.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fischerella sp. PCC 9605 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-BLR / 3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid / Bilirubin IX alpha


Mass: 584.662 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H36N4O6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.81 Å3/Da / Density % sol: 56.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M BICINE (pH 8.0), 181.8 mM NaCl, 9% 2-propanol, 23~34.5% PEG1500

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.349→37.43 Å / Num. obs: 17035 / % possible obs: 89.86 % / Redundancy: 4.5 % / CC1/2: 1 / Net I/σ(I): 34.28
Reflection shellResolution: 3.35→3.45 Å / Num. unique obs: 867 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BAP

6bap


Resolution: 3.35→37.43 Å / SU ML: 0.517 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 31.1142
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2968 1704 10 %
Rwork0.2799 15331 -
obs0.2816 17035 89.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.75 Å2
Refinement stepCycle: LAST / Resolution: 3.35→37.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7344 0 86 0 7430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00267596
X-RAY DIFFRACTIONf_angle_d0.636110339
X-RAY DIFFRACTIONf_chiral_restr0.04491171
X-RAY DIFFRACTIONf_plane_restr0.00451317
X-RAY DIFFRACTIONf_dihedral_angle_d14.02642814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.450.448870.3947780X-RAY DIFFRACTION55.61
3.45-3.560.37961260.37241137X-RAY DIFFRACTION80.29
3.56-3.690.34451370.34241229X-RAY DIFFRACTION86.4
3.69-3.830.31741380.32621244X-RAY DIFFRACTION88.19
3.83-4.010.33341360.3061231X-RAY DIFFRACTION86.41
4.01-4.220.32211450.28071296X-RAY DIFFRACTION91.55
4.22-4.480.29131530.2561385X-RAY DIFFRACTION97.9
4.48-4.830.25491530.23881373X-RAY DIFFRACTION96.95
4.83-5.310.27431560.2651405X-RAY DIFFRACTION98.3
5.31-6.080.30021530.2661376X-RAY DIFFRACTION96.83
6.08-7.650.27091580.26891426X-RAY DIFFRACTION99.56
7.65-37.430.20581620.20061449X-RAY DIFFRACTION99.63

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