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- PDB-3v57: Crystal Structure of the B-phycoerythrin from the red algae Porph... -

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Basic information

Entry
Database: PDB / ID: 3v57
TitleCrystal Structure of the B-phycoerythrin from the red algae Porphyridium Cruentum at pH8
Components
  • Phycoerythrin alpha subunit
  • Phycoerythrin beta subunit
KeywordsPHOTOSYNTHESIS / globin-like
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
PHYCOERYTHROBILIN / Phycoerythrin beta subunit / Phycoerythrin alpha subunit / B-phycoerythrin alpha chain / B-phycoerythrin beta chain
Similarity search - Component
Biological speciesPorphyridium purpureum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsCamara-Artigas, A.
CitationJournal: Febs J. / Year: 2012
Title: pH-dependent structural conformations of B-phycoerythrin from Porphyridium cruentum
Authors: Camara-Artigas, A. / Bacarizo, J. / Andujar-Sanchez, M. / Ortiz-Salmeron, E. / Mesa-Valle, C. / Cuadri, C. / Martin-Garcia, J.M. / Martinez-Rodriguez, S. / Mazzuca-Sobczuk, T. / Ibanez, M.J. / Allen, J.P.
History
DepositionDec 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_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_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: Phycoerythrin alpha subunit
B: Phycoerythrin beta subunit
C: Phycoerythrin alpha subunit
D: Phycoerythrin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,18419
Polymers72,8164
Non-polymers6,36715
Water9,890549
1
A: Phycoerythrin alpha subunit
B: Phycoerythrin beta subunit
hetero molecules

A: Phycoerythrin alpha subunit
B: Phycoerythrin beta subunit
hetero molecules

A: Phycoerythrin alpha subunit
B: Phycoerythrin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,92030
Polymers109,2256
Non-polymers9,69524
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area30610 Å2
ΔGint-344 kcal/mol
Surface area42650 Å2
MethodPISA
2
C: Phycoerythrin alpha subunit
D: Phycoerythrin beta subunit
hetero molecules

C: Phycoerythrin alpha subunit
D: Phycoerythrin beta subunit
hetero molecules

C: Phycoerythrin alpha subunit
D: Phycoerythrin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,63127
Polymers109,2256
Non-polymers9,40721
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area30730 Å2
ΔGint-343 kcal/mol
Surface area41510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.110, 187.110, 59.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Phycoerythrin alpha subunit


Mass: 17824.029 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: E2IH77, UniProt: P11392*PLUS
#2: Protein Phycoerythrin beta subunit


Mass: 18584.182 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: E2IH76, UniProt: P11393*PLUS
#3: Chemical
ChemComp-PEB / PHYCOERYTHROBILIN


Mass: 588.694 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 298 K / Method: counter-diffusion in capillary / pH: 8
Details: 3M ammonium sulphate, 0.1M Tris, pH 8, counter-diffusion in capillary, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionRedundancy: 4.3 % / Av σ(I) over netI: 8.2 / Number: 367561 / Rsym value: 0.072 / D res high: 1.7 Å / D res low: 93.555 Å / Num. obs: 84772 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.3819.8195.110.0340.0344.7
3.85.3899.410.0420.0424.7
3.13.898.110.0450.0453.9
2.693.110010.0580.0584.3
2.42.6910010.0730.0734.4
2.192.410010.0980.0984.4
2.032.1999.910.1380.1384.4
1.92.0399.910.2220.2224.3
1.791.999.910.3710.3714.3
1.71.7910010.5530.5534.3
ReflectionResolution: 1.7→93.555 Å / Num. all: 84772 / Num. obs: 84772 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 20.514 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.794.30.5531.453036124510.553100
1.79-1.94.30.3712.150624117570.37199.9
1.9-2.034.30.2223.548112110810.22299.9
2.03-2.194.40.1385.544941102480.13899.9
2.19-2.44.40.0987.54143194410.098100
2.4-2.694.40.0739.93738285540.073100
2.69-3.14.30.058123260975540.058100
3.1-3.83.90.04514.52450162360.04598.1
3.8-5.384.70.04215.52296348890.04299.4
5.38-19.8064.70.03419.41196225610.03495.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.9 Å35.8 Å
Translation1.9 Å35.8 Å

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Processing

Software
NameVersionClassificationNB
MOSFLM3.3.20data reduction
SCALA3.3.20data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LIA

1lia


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.2121 / WRfactor Rwork: 0.1748 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.875 / SU B: 2.118 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1013 / SU Rfree: 0.1028 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.101 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 4242 5 %RANDOM
Rwork0.1768 ---
all0.1787 85094 --
obs0.1787 84772 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.81 Å2 / Biso mean: 22.1274 Å2 / Biso min: 10.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.11 Å20 Å2
2---0.22 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5088 0 455 549 6092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.025678
X-RAY DIFFRACTIONr_angle_refined_deg2.512.0587750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7825694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.58223.761218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77915852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.261540
X-RAY DIFFRACTIONr_chiral_restr0.130.2847
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.024386
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 317 -
Rwork0.244 6034 -
all-6351 -
obs--99.94 %

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