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- PDB-8or7: Structure of a far-red induced allophycocyanin from Chroococcidio... -

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Basic information

Entry
Database: PDB / ID: 8or7
TitleStructure of a far-red induced allophycocyanin from Chroococcidiopsis thermalis sp. PCC 7203
Components
  • Allophycocyanin beta subunit apoprotein
  • Phycocyanin
KeywordsPHOTOSYNTHESIS / Phycobiliprotein / Allophycocyanin / Far-red light photoacclimation
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Allophycocyanin, beta subunit / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / : / Allophycocyanin beta subunit apoprotein / Phycocyanin
Similarity search - Component
Biological speciesChroococcidiopsis thermalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsZhou, L.J. / Hoeppner, A. / Wang, Y.Q. / Zhao, K.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31861143029 China
CitationJournal: Photosynth.Res. / Year: 2024
Title: Crystallographic and biochemical analyses of a far-red allophycocyanin to address the mechanism of the super-red-shift.
Authors: Zhou, L.J. / Hoppner, A. / Wang, Y.Q. / Hou, J.Y. / Scheer, H. / Zhao, K.H.
History
DepositionApr 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Dec 11, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Allophycocyanin beta subunit apoprotein
D: Allophycocyanin beta subunit apoprotein
A: Phycocyanin
C: Phycocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,25515
Polymers73,4554
Non-polymers2,79911
Water362
1
B: Allophycocyanin beta subunit apoprotein
C: Phycocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2719
Polymers36,7282
Non-polymers1,5447
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-65 kcal/mol
Surface area15440 Å2
2
A: Phycocyanin
hetero molecules

D: Allophycocyanin beta subunit apoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9836
Polymers36,7282
Non-polymers1,2564
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area5420 Å2
ΔGint-70 kcal/mol
Surface area15940 Å2
Unit cell
Length a, b, c (Å)130.540, 130.540, 106.496
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 2 types, 4 molecules BDAC

#1: Protein Allophycocyanin beta subunit apoprotein


Mass: 18553.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis (bacteria) / Gene: Chro_1033 / Production host: Escherichia coli (E. coli) / References: UniProt: K9TVG8
#2: Protein Phycocyanin


Mass: 18174.623 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis (bacteria) / Gene: Chro_1032 / Production host: Escherichia coli (E. coli) / References: UniProt: K9TX42

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Non-polymers , 4 types, 13 molecules

#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.57 Å3/Da / Density % sol: 65.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.5 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 1.0 M lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.57→77.52 Å / Num. obs: 32743 / % possible obs: 100 % / Redundancy: 18.5 % / CC1/2: 1 / Rmerge(I) obs: 0.091 / Net I/σ(I): 20.3
Reflection shellResolution: 2.57→2.71 Å / Redundancy: 16.9 % / Rmerge(I) obs: 1.217 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4760 / CC1/2: 0.843 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
xia2data reduction
pointlessdata scaling
ARP/wARPARP/wARP 8.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→77.52 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.921 / SU B: 12.216 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.612 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24016 1240 4.9 %RANDOM
Rwork0.17775 ---
obs0.18093 24255 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.646 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.08 Å2-0 Å2
2---0.17 Å20 Å2
3---0.54 Å2
Refinement stepCycle: 1 / Resolution: 2.8→77.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4986 0 191 2 5179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125256
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165012
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.6487132
X-RAY DIFFRACTIONr_angle_other_deg0.5061.56511486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7765636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.249568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.57710902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021178
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_it7.637.2022556
X-RAY DIFFRACTIONr_mcbond_other7.6267.2022556
X-RAY DIFFRACTIONr_mcangle_it10.212.9453188
X-RAY DIFFRACTIONr_mcangle_other10.19912.9453189
X-RAY DIFFRACTIONr_scbond_it9.0987.8922700
X-RAY DIFFRACTIONr_scbond_other8.9217.882689
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.35814.1563927
X-RAY DIFFRACTIONr_long_range_B_refined15.04588.7321692
X-RAY DIFFRACTIONr_long_range_B_other15.04588.7221691
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 90 -
Rwork0.259 1801 -
obs--100 %

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