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- PDB-4po5: Crystal structure of allophycocyanin B from Synechocystis PCC 6803 -

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Basic information

Entry
Database: PDB / ID: 4po5
TitleCrystal structure of allophycocyanin B from Synechocystis PCC 6803
Components
  • Allophycocyanin beta chain
  • Allophycocyanin subunit alpha-B
KeywordsPHOTOSYNTHESIS / alpha-helical phycobiliprotein / light harvesting / phycocyanobilin / methylation on Asn71 in ApcB subunit / phycobilisome
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
PHYCOCYANOBILIN / Allophycocyanin subunit alpha-B / Allophycocyanin beta chain
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.751 Å
AuthorsPang, P.P. / Dong, L.L. / Sun, Y.F. / Zeng, X.L. / Ding, W.L. / Scheer, H. / Yang, X. / Zhao, K.H.
CitationJournal: Acta Crystallogr D Biol Crystallogr / Year: 2014
Title: The structure of allophycocyanin B from Synechocystis PCC 6803 reveals the structural basis for the extreme redshift of the terminal emitter in phycobilisomes.
Authors: Pan Pan Peng / Liang Liang Dong / Ya Fang Sun / Xiao Li Zeng / Wen Long Ding / Hugo Scheer / Xiaojing Yang / Kai Hong Zhao /
Abstract: Allophycocyanin B (AP-B) is one of the two terminal emitters in phycobilisomes, the unique light-harvesting complexes of cyanobacteria and red algae. Its low excitation-energy level and the ...Allophycocyanin B (AP-B) is one of the two terminal emitters in phycobilisomes, the unique light-harvesting complexes of cyanobacteria and red algae. Its low excitation-energy level and the correspondingly redshifted absorption and fluorescence emission play an important role in funnelling excitation energy from the hundreds of chromophores of the extramembraneous phycobilisome to the reaction centres within the photosynthetic membrane. In the absence of crystal structures of these low-abundance terminal emitters, the molecular basis for the extreme redshift and directional energy transfer is largely unknown. Here, the crystal structure of trimeric AP-B [(ApcD/ApcB)3] from Synechocystis sp. PCC 6803 at 1.75 Å resolution is reported. In the crystal lattice, eight trimers of AP-B form a porous, spherical, 48-subunit assembly of 193 Å in diameter with an internal cavity of 1.1 × 10(6) Å(3). While the overall structure of trimeric AP-B is similar to those reported for many other phycobiliprotein trimers, the chromophore pocket of the α-subunit, ApcD, has more bulky residues that tightly pack the phycocyanobilin (PCB). Ring D of the chromophores is further stabilized by close interactions with ApcB from the adjacent monomer. The combined contributions from both subunits render the conjugated rings B, C and D of the PCB in ApcD almost perfectly coplanar. Together with mutagenesis data, it is proposed that the enhanced planarity effectively extends the conjugation system of PCB and leads to the redshifted absorption (λmax = 669 nm) and fluorescence emission (679 nm) of the ApcD chromophore in AP-B, thereby enabling highly efficient energy transfer from the phycobilisome core to the reaction centres.
History
DepositionFeb 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Allophycocyanin subunit alpha-B
B: Allophycocyanin beta chain
C: Allophycocyanin subunit alpha-B
D: Allophycocyanin beta chain
E: Allophycocyanin subunit alpha-B
F: Allophycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,59433
Polymers108,0456
Non-polymers5,54927
Water21,5821198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23760 Å2
ΔGint-396 kcal/mol
Surface area40580 Å2
MethodPISA
2
A: Allophycocyanin subunit alpha-B
B: Allophycocyanin beta chain
C: Allophycocyanin subunit alpha-B
D: Allophycocyanin beta chain
E: Allophycocyanin subunit alpha-B
F: Allophycocyanin beta chain
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)908,754264
Polymers864,35848
Non-polymers44,396216
Water86548
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area204190 Å2
ΔGint-3349 kcal/mol
Surface area310480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.293, 184.293, 260.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Allophycocyanin subunit alpha-B /


Mass: 18769.273 Da / Num. of mol.: 3 / Fragment: ApcD subunit / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. (bacteria) / Strain: Synechocystis PCC 6803 / References: UniProt: P72870
#2: Protein Allophycocyanin beta chain


Mass: 17245.629 Da / Num. of mol.: 3 / Fragment: ApcB subunit / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. (bacteria) / Strain: Synechocystis PCC 6803 / References: UniProt: Q01952
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1198 / Source method: isolated from a natural source / Formula: H2O

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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: 5.13 Å3/Da / Density % sol: 76.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1M sodium cacodylate (pH 6.5) and 30% (w/v) PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 6, 2014
RadiationMonochromator: diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 222743 / Num. obs: 219625 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 23.8

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Processing

Software
NameVersionClassification
MD2data collection
PHASERphasing
PHENIX(phenix.refine: dev_1610)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B33

1b33


Resolution: 1.751→32.579 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 19.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 11049 5.03 %5% reflection from each resolution shell are selected for cross validation.
Rwork0.1703 ---
obs0.1714 219453 98.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.751→32.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7440 0 363 1198 9001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098209
X-RAY DIFFRACTIONf_angle_d1.50711203
X-RAY DIFFRACTIONf_dihedral_angle_d13.1693028
X-RAY DIFFRACTIONf_chiral_restr0.0391217
X-RAY DIFFRACTIONf_plane_restr0.0061429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.751-1.77090.31223700.30326726X-RAY DIFFRACTION96
1.7709-1.79170.30943520.27946775X-RAY DIFFRACTION97
1.7917-1.81360.28143520.26296784X-RAY DIFFRACTION97
1.8136-1.83650.27893410.24686820X-RAY DIFFRACTION98
1.8365-1.86070.25583260.23566881X-RAY DIFFRACTION98
1.8607-1.88620.23793780.2216855X-RAY DIFFRACTION99
1.8862-1.91310.22813730.21686917X-RAY DIFFRACTION99
1.9131-1.94170.23413720.22276913X-RAY DIFFRACTION99
1.9417-1.9720.23823710.21756917X-RAY DIFFRACTION99
1.972-2.00440.21813770.19916929X-RAY DIFFRACTION99
2.0044-2.03890.20713830.18056900X-RAY DIFFRACTION99
2.0389-2.0760.18573780.17926954X-RAY DIFFRACTION99
2.076-2.11590.21583730.17986956X-RAY DIFFRACTION99
2.1159-2.15910.21513920.17666939X-RAY DIFFRACTION99
2.1591-2.2060.19313400.16786985X-RAY DIFFRACTION99
2.206-2.25730.18263810.16526949X-RAY DIFFRACTION100
2.2573-2.31380.18474170.16546961X-RAY DIFFRACTION99
2.3138-2.37630.20353460.16486992X-RAY DIFFRACTION99
2.3763-2.44620.18243610.16216988X-RAY DIFFRACTION100
2.4462-2.52510.19293620.17037060X-RAY DIFFRACTION99
2.5251-2.61530.21793890.17236933X-RAY DIFFRACTION99
2.6153-2.720.2233820.18056971X-RAY DIFFRACTION99
2.72-2.84370.19583640.18917041X-RAY DIFFRACTION99
2.8437-2.99360.21753590.19247001X-RAY DIFFRACTION99
2.9936-3.1810.21693750.19187017X-RAY DIFFRACTION99
3.181-3.42630.20383660.17186993X-RAY DIFFRACTION99
3.4263-3.77070.17993250.14817057X-RAY DIFFRACTION99
3.7707-4.31520.13733980.12457021X-RAY DIFFRACTION98
4.3152-5.43270.14233820.12327029X-RAY DIFFRACTION98
5.4327-32.58430.16963640.15387140X-RAY DIFFRACTION96
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)
15.0166-0.42180.20230.27120.09230.4290.0068-0.1086-0.52660.03080.00180.13530.0808-0.046-0.01590.15840.0134-0.00420.13680.02410.230314.85334.674368.0086
23.1486-1.11851.54390.4266-0.53651.3431-0.0370.0150.081-0.003-0.0377-0.1217-0.01980.14170.07870.1222-0.04010.01520.17980.00210.1965-15.921151.572163.211
31.7951.2717-1.69811.6384-1.40652.1379-0.16540.30290.0342-0.25690.20430.05750.1438-0.233-0.00620.1633-0.0465-0.01650.20390.0020.1554-38.027257.985735.0133
43.28470.6697-1.33450.6285-0.34260.53970.0225-0.2182-0.07390.06910.00050.05480.021-0.0103-0.02950.2014-0.0040.01150.19740.03260.1131-10.822178.349125.3225
51.0495-0.80931.54931.5283-1.60093.02590.10170.1631-0.0147-0.1288-0.1448-0.12480.2860.38240.01650.18210.04020.0240.21330.0080.135823.266872.784814.053
60.18250.3553-0.1341.6443-1.94062.8926-0.00180.11450.0850.00250.06060.0979-0.105-0.1202-0.0550.14670.0457-0.0240.17180.01770.188526.728662.577147.7989
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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