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- PDB-1kn1: Crystal structure of allophycocyanin -

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Basic information

Entry
Database: PDB / ID: 1kn1
TitleCrystal structure of allophycocyanin
Components(Allophycocyanin) x 2
KeywordsELECTRON TRANSPORT / helix-turn-helix
Function / homology
Function and homology information


phycobilisome / chloroplast 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 speciesPorphyra yezoensis (susabi-nori)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLiang, D.C. / Liu, J.Y. / Jiang, T. / Zhang, J.P. / Chang, W.R.
CitationJournal: J.BIOL.CHEM. / Year: 1999
Title: Crystal structure of Allophycocyanin from red algae Porphyra yezoensis at 2.2 A resolution
Authors: Liu, J.Y. / Jiang, T. / Zhang, J.P. / Liang, D.C.
History
DepositionDec 18, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)36,0214
Polymers34,8442
Non-polymers1,1772
Water3,045169
1
A: Allophycocyanin
B: Allophycocyanin
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)216,12624
Polymers209,06212
Non-polymers7,06412
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area50390 Å2
ΔGint-451 kcal/mol
Surface area71890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.300, 105.300, 189.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Allophycocyanin


Mass: 17383.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyra yezoensis (susabi-nori) / References: UniProt: P59856*PLUS
#2: Protein Allophycocyanin


Mass: 17459.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Porphyra yezoensis (susabi-nori) / References: UniProt: P59857*PLUS
#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.: 169 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN (CHAIN A AND B) DOES NOT CURRENTLY EXIST.

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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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: Ammonium sulfate, pH 7.3, Vapor diffusion, hanging drop, temperature 298K
Crystal grow
*PLUS
Details: Liu, J.Y., (1998) Acta Crystallogr., D54, 662.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
14 mg/mlprotein1drop
20.25 M1dropMgCl2
30.4 Mammonium sulfate1drop
450 mMHEPES1droppH7.3
50.4 M1reservoirMgCl2
61.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS X200B / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 20096 / Num. obs: 20096 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.3
Reflection shellResolution: 2.2→2.3 Å / Mean I/σ(I) obs: 2.1 / % possible all: 65
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 87 %

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1ALL

1all


Resolution: 2.2→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1537 10 %RANDOM
Rwork0.193 ---
all-15368 --
obs-15368 --
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2441 0 86 169 2696
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg2.9
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 18059
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2.9

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