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- PDB-1b33: STRUCTURE OF LIGHT HARVESTING COMPLEX OF ALLOPHYCOCYANIN ALPHA AN... -

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Entry
Database: PDB / ID: 1b33
TitleSTRUCTURE OF LIGHT HARVESTING COMPLEX OF ALLOPHYCOCYANIN ALPHA AND BETA CHAINS/CORE-LINKER COMPLEX AP*LC7.8
Components
  • (ALLOPHYCOCYANIN, ...) x 2
  • PHYCOBILISOME 7.8 KD LINKER POLYPEPTIDE
KeywordsPHOTOSYNTHESIS / LIGHT-HARVESTING PROTEIN / CYANOBACTERIA / ALLOPHYCOCYANIN / LINKER POLYPEPTIDES / COMPLEX STRUCTURE
Function / homology
Function and homology information


: / : / phycobilisome / photosynthesis
Similarity search - Function
Allophycocyanin linker chain (domain) / Allophycocyanin linker protein / Allophycocyanin linker chain / Allophycocyanin, beta subunit / Phycocyanins / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Phycobilisome, alpha/beta subunit ...Allophycocyanin linker chain (domain) / Allophycocyanin linker protein / Allophycocyanin linker chain / Allophycocyanin, beta subunit / Phycocyanins / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Dna Ligase; domain 1 / Globin-like / Globin-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / BORATE ION / PHYCOCYANOBILIN / Allophycocyanin alpha chain / Allophycocyanin beta chain / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
Similarity search - Component
Biological speciesMastigocladus laminosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsReuter, W. / Wiegand, G. / Huber, R. / Than, M.E.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structural analysis at 2.2 A of orthorhombic crystals presents the asymmetry of the allophycocyanin-linker complex, AP.LC7.8, from phycobilisomes of Mastigocladus laminosus.
Authors: Reuter, W. / Wiegand, G. / Huber, R. / Than, M.E.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Isolation, Crystallization, Crystal Structure Analysis and Refinement of Allophycocyanin from the Cyanobacterium Spirulina Platensis at 2.3 A Resolution
Authors: Brejc, K. / Ficner, R. / Huber, R. / Steinbacher, S.
#2: Journal: Hoppe-Seyler's Z.Physiol.Chem. / Year: 1984
Title: Minor Polypeptides from the Cyanobacterium Mastigocladus Laminosus
Authors: Fueglistaller, P. / Ruembli, R. / Suter, F. / Zuber, H.
#3: Journal: Hoppe-Seyler's Z.Physiol.Chem. / Year: 1981
Title: The Complete Amino Acid Sequence of Both Subunits of Allophycocyanin, a Light Harvesting Protein-Pigment Complex from the Cyanobacterium Mastigocladus Laminosus
Authors: Sidler, W. / Gysi, J. / Isker, E. / Zuber, H.
History
DepositionDec 15, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALLOPHYCOCYANIN, ALPHA CHAIN
B: ALLOPHYCOCYANIN, BETA CHAIN
C: ALLOPHYCOCYANIN, ALPHA CHAIN
D: ALLOPHYCOCYANIN, BETA CHAIN
E: ALLOPHYCOCYANIN, ALPHA CHAIN
F: ALLOPHYCOCYANIN, BETA CHAIN
N: PHYCOBILISOME 7.8 KD LINKER POLYPEPTIDE
H: ALLOPHYCOCYANIN, ALPHA CHAIN
I: ALLOPHYCOCYANIN, BETA CHAIN
J: ALLOPHYCOCYANIN, ALPHA CHAIN
K: ALLOPHYCOCYANIN, BETA CHAIN
L: ALLOPHYCOCYANIN, ALPHA CHAIN
M: ALLOPHYCOCYANIN, BETA CHAIN
O: PHYCOBILISOME 7.8 KD LINKER POLYPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,12730
Polymers222,75914
Non-polymers7,36816
Water24,2121344
1
A: ALLOPHYCOCYANIN, ALPHA CHAIN
B: ALLOPHYCOCYANIN, BETA CHAIN
C: ALLOPHYCOCYANIN, ALPHA CHAIN
D: ALLOPHYCOCYANIN, BETA CHAIN
E: ALLOPHYCOCYANIN, ALPHA CHAIN
F: ALLOPHYCOCYANIN, BETA CHAIN
N: PHYCOBILISOME 7.8 KD LINKER POLYPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,05715
Polymers111,3807
Non-polymers3,6788
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25910 Å2
ΔGint-220 kcal/mol
Surface area39170 Å2
MethodPISA
2
H: ALLOPHYCOCYANIN, ALPHA CHAIN
I: ALLOPHYCOCYANIN, BETA CHAIN
J: ALLOPHYCOCYANIN, ALPHA CHAIN
K: ALLOPHYCOCYANIN, BETA CHAIN
L: ALLOPHYCOCYANIN, ALPHA CHAIN
M: ALLOPHYCOCYANIN, BETA CHAIN
O: PHYCOBILISOME 7.8 KD LINKER POLYPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,07015
Polymers111,3807
Non-polymers3,6908
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25480 Å2
ΔGint-227 kcal/mol
Surface area39160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.120, 151.900, 137.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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ALLOPHYCOCYANIN, ... , 2 types, 12 molecules ACEHJLBDFIKM

#1: Protein
ALLOPHYCOCYANIN, ALPHA CHAIN /


Mass: 17138.398 Da / Num. of mol.: 6 / Fragment: ALPHA CHAINS / Source method: isolated from a natural source
Details: LONG TIME LABORATORY CULTURE, ADAPTED TO LOW TEMPERATURE
Source: (natural) Mastigocladus laminosus (bacteria) / Cell line: PCC 7603 / Cellular location: CYTOPLASM, PHYCOBILISOME CORE / References: UniProt: P00315
#2: Protein
ALLOPHYCOCYANIN, BETA CHAIN /


Mass: 17403.822 Da / Num. of mol.: 6 / Fragment: BETA CHAINS / Source method: isolated from a natural source
Details: LONG TIME LABORATORY CULTURE, ADAPTED TO LOW TEMPERATURE
Source: (natural) Mastigocladus laminosus (bacteria) / Cell line: PCC 7603 / Cellular location: CYTOPLASM, PHYCOBILISOME CORE / References: UniProt: P00318

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Protein , 1 types, 2 molecules NO

#3: Protein PHYCOBILISOME 7.8 KD LINKER POLYPEPTIDE / ALLOPHYCOCYANIN-ASSOCIATED / CORE (LC 7.8) / APC / AP 664 / AP*LC8.9 / AP*LC10 / LC8.9 / LC10


Mass: 7753.017 Da / Num. of mol.: 2 / Fragment: PEPTIDE LINKER / Source method: isolated from a natural source
Details: LONG TIME LABORATORY CULTURE, ADAPTED TO LOW TEMPERATURE
Source: (natural) Mastigocladus laminosus (bacteria) / Cell line: PCC 7603 / Cellular location: CYTOPLASM, PHYCOBILISOME CORE / References: UniProt: P20116

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Non-polymers , 4 types, 1360 molecules

#4: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H34N4O6
#5: Chemical
ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C33H40N4O6
#6: Chemical
ChemComp-BO4 / BORATE ION / Borate


Mass: 78.840 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: BH4O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1344 / 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: 4.07 Å3/Da / Density % sol: 70 %
Crystal growpH: 7.9 / Details: pH 7.9
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 27 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
2640 mM1reservoircan be replaced by 360mM MgSO4Li2SO4
38 %(w/v)PEG60001reservoiror 6%(w/v)
424 mMTris-boric1reservoiror 18mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.06
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRROR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. obs: 180426 / % possible obs: 96.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 36.77 Å2 / Rsym value: 0.069 / Net I/σ(I): 8.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.318 / % possible all: 96.6
Reflection
*PLUS
Num. measured all: 637968 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 96.6 % / Rmerge(I) obs: 0.318

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ALL

1all


Resolution: 2.3→25 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
Details: OCCUPANCY AND B-FACTOR ARE SET TO ZERO FOR ALL ATOMS, THAT ARE NOT DEFINED IN THE FINAL 2FO-FC ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 -4.82 %20 THIN SHELLS
Rwork0.211 ---
obs0.211 180369 96.48 %-
all-180369 --
Displacement parametersBiso mean: 34.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15622 0 536 1344 17502
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.806
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d17.92
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.373
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.24 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3246 451 4.87 %
Rwork0.3074 6773 -
obs--76.96 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 25 Å / σ(F): 0 / % reflection Rfree: 4.82 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg17.92
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.373
LS refinement shell
*PLUS
Rfactor obs: 0.3074

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