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- PDB-5b13: Crystal structure of phycoerythrin -

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Basic information

Entry
Database: PDB / ID: 5b13
TitleCrystal structure of phycoerythrin
Components
  • Phycoerythrin alpha subunit
  • Phycoerythrin beta subunit
KeywordsPHOTOSYNTHESIS / Phycobiliprotein
Function / homology
Function and homology information


phycobilisome / chloroplast thylakoid membrane / photosynthesis
Similarity search - Function
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 / PHYCOUROBILIN / Phycoerythrin beta subunit / Phycoerythrin alpha subunit
Similarity search - Component
Biological speciesPalmaria palmata (dulse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.094 Å
AuthorsTanaka, Y. / Gai, Z. / Kishimura, H.
CitationJournal: J FOOD BIOCHEM. / Year: 2016
Title: Structural properties of phycoerythrin from dulse palmaria palmata
Authors: Miyabe, Y. / Furuta, T. / Takeda, T. / Kanno, G. / Shimizu, T. / Tanaka, Y. / Gai, Z. / Yasui, H. / Kishimura, H.
History
DepositionNov 18, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn
Item: _citation.country / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phycoerythrin alpha subunit
G: Phycoerythrin beta subunit
B: Phycoerythrin alpha subunit
C: Phycoerythrin alpha subunit
D: Phycoerythrin alpha subunit
E: Phycoerythrin alpha subunit
F: Phycoerythrin alpha subunit
H: Phycoerythrin beta subunit
I: Phycoerythrin beta subunit
J: Phycoerythrin beta subunit
K: Phycoerythrin beta subunit
L: Phycoerythrin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,16942
Polymers216,49712
Non-polymers17,67330
Water32,5711808
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area71690 Å2
ΔGint-608 kcal/mol
Surface area70710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.500, 111.850, 112.670
Angle α, β, γ (deg.)90.00, 91.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Phycoerythrin alpha subunit


Mass: 17657.760 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: CYCs are covalently attached to the polypeptide chain.
Source: (natural) Palmaria palmata (dulse) / References: UniProt: F2ZAL8
#2: Protein
Phycoerythrin beta subunit


Mass: 18425.002 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Details: CYC and PUB are covalently attached to the polypeptide chain.
Source: (natural) Palmaria palmata (dulse) / References: UniProt: F2ZAL7
#3: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: C33H40N4O6
#4: Chemical
ChemComp-PUB / PHYCOUROBILIN


Mass: 590.710 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C33H42N4O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1808 / Source method: isolated from a natural source / Formula: H2O
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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium acetate, PEG4000 / PH range: 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 135827 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rsym value: 0.116 / Net I/σ(I): 11.21
Reflection shellResolution: 2.09→2.22 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2.13 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.094→48.933 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2365 6792 5 %
Rwork0.1976 --
obs0.1996 135817 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.094→48.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15114 0 1290 1808 18212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316740
X-RAY DIFFRACTIONf_angle_d1.31822890
X-RAY DIFFRACTIONf_dihedral_angle_d15.3955976
X-RAY DIFFRACTIONf_chiral_restr0.0242442
X-RAY DIFFRACTIONf_plane_restr0.0032910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0942-2.1180.32792010.27473808X-RAY DIFFRACTION89
2.118-2.14290.30832270.25824327X-RAY DIFFRACTION100
2.1429-2.1690.32832250.25414262X-RAY DIFFRACTION100
2.169-2.19650.34492240.25574271X-RAY DIFFRACTION100
2.1965-2.22540.28972280.24414327X-RAY DIFFRACTION100
2.2254-2.25590.29122240.23384256X-RAY DIFFRACTION100
2.2559-2.28810.28892290.22764339X-RAY DIFFRACTION100
2.2881-2.32220.30362250.23254281X-RAY DIFFRACTION100
2.3222-2.35850.2822260.22344289X-RAY DIFFRACTION100
2.3585-2.39720.25792270.21544316X-RAY DIFFRACTION100
2.3972-2.43850.28022270.21114325X-RAY DIFFRACTION100
2.4385-2.48290.26712280.20574328X-RAY DIFFRACTION100
2.4829-2.53060.28532270.20994302X-RAY DIFFRACTION100
2.5306-2.58230.25472250.20384276X-RAY DIFFRACTION100
2.5823-2.63840.24312260.20224306X-RAY DIFFRACTION100
2.6384-2.69980.23672290.20534342X-RAY DIFFRACTION100
2.6998-2.76730.27652250.21414276X-RAY DIFFRACTION100
2.7673-2.84210.2862280.2114326X-RAY DIFFRACTION100
2.8421-2.92570.25722260.20374311X-RAY DIFFRACTION100
2.9257-3.02020.22732280.19034321X-RAY DIFFRACTION100
3.0202-3.12810.23152280.20264327X-RAY DIFFRACTION100
3.1281-3.25330.24792260.20584308X-RAY DIFFRACTION100
3.2533-3.40130.23792290.20224351X-RAY DIFFRACTION100
3.4013-3.58060.22962260.19134290X-RAY DIFFRACTION100
3.5806-3.80490.20032290.17874342X-RAY DIFFRACTION100
3.8049-4.09850.19242280.16934335X-RAY DIFFRACTION100
4.0985-4.51070.16792290.15574352X-RAY DIFFRACTION100
4.5107-5.16280.20962290.16774354X-RAY DIFFRACTION100
5.1628-6.50220.1822300.18554361X-RAY DIFFRACTION100
6.5022-48.94680.17762330.1644416X-RAY DIFFRACTION99

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