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- PDB-6hrk: Structure of a far-red fluorescent biliprotein derived from a far... -

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Basic information

Entry
Database: PDB / ID: 6hrk
TitleStructure of a far-red fluorescent biliprotein derived from a far-red induced allophycocyanin F subunit from a thermophilic cyanobacterium Chroococcidiopsis thermalis
ComponentsAllophycocyanin beta-18 subunit apoprotein
KeywordsFLUORESCENT PROTEIN / biliprotein / allophycocyanin
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Allophycocyanin, beta subunit / Phycocyanins / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / Allophycocyanin beta-18 subunit apoprotein
Similarity search - Component
Biological speciesChroococcidiopsis thermalis PCC 7203 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsHou, Y.-N. / Hoeppner, A. / Ding, W.-L. / Gaertner, W. / Zhao, K.-H.
CitationJournal: Protein Sci., Suppl.: Diskette Appendix To V. , No. , [Month], Filename:
Year: 2022
Title: Control of a far-red/near-infrared spectral switch in an artificial fluorescent biliprotein derived from allophycocyanin
Authors: Hou, Y.N. / Hoppner, A. / Rao, A.G. / Lahav, Y. / Kumar Das, P. / Ding, W.L. / Jiang, X.X. / Hu, J.L. / Schapiro, I. / Noy, D. / Zhao, K.H.
History
DepositionSep 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 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: Allophycocyanin beta-18 subunit apoprotein
B: Allophycocyanin beta-18 subunit apoprotein
C: Allophycocyanin beta-18 subunit apoprotein
D: Allophycocyanin beta-18 subunit apoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1118
Polymers65,7804
Non-polymers2,3314
Water00
1
A: Allophycocyanin beta-18 subunit apoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0282
Polymers16,4451
Non-polymers5831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Allophycocyanin beta-18 subunit apoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0282
Polymers16,4451
Non-polymers5831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Allophycocyanin beta-18 subunit apoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0282
Polymers16,4451
Non-polymers5831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Allophycocyanin beta-18 subunit apoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0282
Polymers16,4451
Non-polymers5831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.248, 74.823, 61.031
Angle α, β, γ (deg.)90.00, 90.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Allophycocyanin beta-18 subunit apoprotein


Mass: 16445.000 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis PCC 7203 (bacteria)
Gene: Chro_1766 / Production host: Escherichia coli (E. coli) / References: UniProt: K9TY40
#2: Chemical
ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H34N4O6
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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (v/v) 2-propanol 0.1 M MES monohydrate pH 6.0 20% (w/v) PEGMME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.52→50 Å / Num. obs: 17506 / % possible obs: 93 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.2956 / Net I/σ(I): 4.28
Reflection shellResolution: 2.52→2.61 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.8865 / Mean I/σ(I) obs: 1.24 / Num. unique obs: 1603 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
xia2data reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CPC

1cpc


Resolution: 2.52→47.39 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.832 / SU B: 8.923 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R Free: 0.094 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33173 870 5 %RANDOM
Rwork0.27412 ---
obs0.27695 16526 92.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.624 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å2-24.98 Å2
2---14 Å20 Å2
3---15.75 Å2
Refinement stepCycle: 1 / Resolution: 2.52→47.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4079 0 172 0 4251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194338
X-RAY DIFFRACTIONr_bond_other_d0.0010.024173
X-RAY DIFFRACTIONr_angle_refined_deg1.4792.0185874
X-RAY DIFFRACTIONr_angle_other_deg3.2793.0029533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8065536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09522.606165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51215696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3981537
X-RAY DIFFRACTIONr_chiral_restr0.0540.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024861
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02944
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6553.6712156
X-RAY DIFFRACTIONr_mcbond_other0.6553.6712155
X-RAY DIFFRACTIONr_mcangle_it1.1785.5022688
X-RAY DIFFRACTIONr_mcangle_other1.1785.5022689
X-RAY DIFFRACTIONr_scbond_it0.4583.6092182
X-RAY DIFFRACTIONr_scbond_other0.4583.6092183
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8045.4073187
X-RAY DIFFRACTIONr_long_range_B_refined2.06428.954979
X-RAY DIFFRACTIONr_long_range_B_other2.06428.954979
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.519→2.584 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 55 -
Rwork0.336 1047 -
obs--79.97 %

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