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- PDB-1all: ALLOPHYCOCYANIN -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1all
TitleALLOPHYCOCYANIN
Components(ALLOPHYCOCYANIN) x 2
KeywordsLIGHT-HARVESTING PROTEIN / PHYCOBILIPROTEIN
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 alpha chain / Allophycocyanin beta chain
Similarity search - Component
Biological speciesArthrospira platensis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.3 Å
AuthorsBrejc, K. / Ficner, R. / Huber, R. / Steinbacher, S.
CitationJournal: 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.
History
DepositionMar 1, 1995Processing site: BNL
Revision 1.0Jul 11, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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
B: ALLOPHYCOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5594
Polymers34,3812
Non-polymers1,1772
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-56 kcal/mol
Surface area14700 Å2
MethodPISA
2
A: ALLOPHYCOCYANIN
B: ALLOPHYCOCYANIN
hetero molecules

A: ALLOPHYCOCYANIN
B: ALLOPHYCOCYANIN
hetero molecules

A: ALLOPHYCOCYANIN
B: ALLOPHYCOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,67612
Polymers103,1436
Non-polymers3,5326
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area20990 Å2
ΔGint-216 kcal/mol
Surface area38860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.900, 101.900, 130.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein ALLOPHYCOCYANIN / APC


Mass: 17107.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CHROMOPHORE PHYCOCYANOBILIN / Source: (natural) Arthrospira platensis (bacteria) / References: UniProt: P72504
#2: Protein ALLOPHYCOCYANIN / APC


Mass: 17273.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CHROMOPHORE PHYCOCYANOBILIN / Source: (natural) Arthrospira platensis (bacteria) / References: UniProt: P72505
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.85 Å3/Da / Density % sol: 54 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlAPC1drop
25 mMpotassium phosphate1drop
30.1 M1reservoirMgCl2
450 mMTris-HCl1reservoir
515 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 268 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→999 Å / Num. obs: 17566 / % possible obs: 95.3 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.07 / Rsym value: 0.022
Reflection shellResolution: 2.3→2.34 Å / % possible all: 68.6
Reflection
*PLUS
Num. measured all: 177454 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 68.6 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.196 --
obs0.196 17135 95.3 %
Displacement parametersBiso mean: 23 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 86 92 2586
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.409
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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

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