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- PDB-3l0f: High resolution structure of C-Phycocyanin from Thermosynechococc... -

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Basic information

Entry
Database: PDB / ID: 3l0f
TitleHigh resolution structure of C-Phycocyanin from Thermosynechococcus elongatus
Components
  • C-phycocyanin alpha chain
  • C-phycocyanin beta chain
KeywordsPHOTOSYNTHESIS / PHOTOSYSTEM II / LIGHT HARVESTING PROTEINS / THERMOSTABILITY / BILE PIGMENT / CHLOROPLAST / CHROMOPHORE / ELECTRON TRANSPORT / MEMBRANE / PHYCOBILISOME / PLASTID / THYLAKOID / TRANSPORT / METHYLATION
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycocyanin, alpha subunit / Phycocyanin, 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 / C-phycocyanin alpha subunit / C-phycocyanin beta subunit
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsFromme, R. / Brune, D. / Fromme, P.
CitationJournal: Iucrj / Year: 2015
Title: Serial femtosecond crystallography of soluble proteins in lipidic cubic phase.
Authors: Fromme, R. / Ishchenko, A. / Metz, M. / Chowdhury, S.R. / Basu, S. / Boutet, S. / Fromme, P. / White, T.A. / Barty, A. / Spence, J.C. / Weierstall, U. / Liu, W. / Cherezov, V.
History
DepositionDec 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _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 1.3Sep 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

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Assembly

Deposited unit
A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4395
Polymers35,6732
Non-polymers1,7663
Water10,323573
1
A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)224,63630
Polymers214,04012
Non-polymers10,59618
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 area60630 Å2
ΔGint-502 kcal/mol
Surface area68180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.100, 187.100, 59.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-295-

HOH

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Components

#1: Protein C-phycocyanin alpha chain


Mass: 17456.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Former name Synechococcus elongatus / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P50032
#2: Protein C-phycocyanin beta chain


Mass: 18216.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: cpcB, tlr1957 / References: UniProt: P50033
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / 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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8 % PEG 2000 , 0.05 M MES, 20 mM MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290-291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2009 / Details: Double crystal, Si(111)
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→42.79 Å / Num. all: 87205 / Num. obs: 86993 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 10.9
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 2.2 / Num. unique all: 12693 / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1KTP and 1JBO

1ktp

1jbo


Resolution: 1.35→19.5 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.926 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.047
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17507 4367 5 %RANDOM
Rwork0.13343 ---
obs0.13553 82594 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.396 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.15 Å20 Å2
2---0.29 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.35→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 129 573 3199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222691
X-RAY DIFFRACTIONr_bond_other_d0.0070.021721
X-RAY DIFFRACTIONr_angle_refined_deg2.6932.0173668
X-RAY DIFFRACTIONr_angle_other_deg1.5834194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7335338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.66224.505111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33515411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8351517
X-RAY DIFFRACTIONr_chiral_restr0.1330.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.020.023071
X-RAY DIFFRACTIONr_gen_planes_other0.0290.02546
X-RAY DIFFRACTIONr_mcbond_it2.671.51667
X-RAY DIFFRACTIONr_mcbond_other1.4141.5683
X-RAY DIFFRACTIONr_mcangle_it3.62122648
X-RAY DIFFRACTIONr_scbond_it5.72131024
X-RAY DIFFRACTIONr_scangle_it7.7464.51018
X-RAY DIFFRACTIONr_rigid_bond_restr2.45634412
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 296 -
Rwork0.271 6097 -
obs--99.86 %

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