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- PDB-3brp: Crystal Structure of C-Phycocyanin from Galdieria sulphuraria -

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Basic information

Entry
Database: PDB / ID: 3brp
TitleCrystal Structure of C-Phycocyanin from Galdieria sulphuraria
Components
  • C-phycocyanin alpha chain
  • C-phycocyanin beta chain
KeywordsPHOTOSYNTHESIS / PHOTOSYSTEM II / LIGHT HARVESTING PROTEINS / RED ALGAE / THERMOSTABILITY / Bile pigment / Chloroplast / Chromophore / Electron transport / Membrane / Phycobilisome / Plastid / Thylakoid / Transport / Methylation
Function / homology
Function and homology information


phycobilisome / chloroplast 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
BILIVERDINE IX ALPHA / C-phycocyanin alpha chain / C-phycocyanin beta chain
Similarity search - Component
Biological speciesGaldieria sulphuraria (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsFromme, R.
CitationJournal: To be Published
Title: Crystal Structure of C-Phycocyanin from Galdieria sulphuraria at 1.85 A
Authors: Fromme, R. / Thangaraj, B. / Vanselow, C. / Fromme, P.
History
DepositionDec 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)37,5235
Polymers35,7752
Non-polymers1,7483
Water6,125340
1
A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)225,13930
Polymers214,65212
Non-polymers10,48818
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 area60360 Å2
MethodPISA
2
A: C-phycocyanin alpha chain
hetero molecules

A: C-phycocyanin alpha chain
hetero molecules

A: C-phycocyanin alpha chain
hetero molecules

B: C-phycocyanin beta chain
hetero molecules

B: C-phycocyanin beta chain
hetero molecules

B: C-phycocyanin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,57015
Polymers107,3266
Non-polymers5,2449
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area24120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.818, 102.818, 172.883
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
11A-549-

HOH

21A-607-

HOH

DetailsTHE DODECAMER IN REMARK 350 REPRESENTS A HEXAMER OF HETERODIMER

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Components

#1: Protein C-phycocyanin alpha chain


Mass: 17520.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: P00306
#2: Protein C-phycocyanin beta chain


Mass: 18254.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) / References: UniProt: P00311
#3: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H34N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATES THAT THE CONFLICTS WITH UNP DATABASE ARE DUE TO DIFFERENT SPECIES. THE SEQUENCE IN ...AUTHOR STATES THAT THE CONFLICTS WITH UNP DATABASE ARE DUE TO DIFFERENT SPECIES. THE SEQUENCE IN UNP ENTRIES ARE ACTURALLY FROM CYANIDIUM CALDARIUM, NOT FROM GALDIERIA SULPHURARIA. REFERENCE: JOURNAL OF PHYCOLOGY 27 (6): 794-796 DEC 1991

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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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 9.5% PEG 2000,0.1M HEPES, 0.1M MGCl2, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 30304 / Num. obs: 30145 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 15.5
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.516 / Rsym value: 0.538 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
ARPmodel building
WARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KTP

1ktp


Resolution: 1.85→10 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.247 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.14
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23127 1521 5.1 %RANDOM
Rwork0.18205 ---
obs0.18466 28415 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.185 Å2
Baniso -1Baniso -2Baniso -3
1--2.04 Å2-1.02 Å20 Å2
2---2.04 Å20 Å2
3---3.07 Å2
Refinement stepCycle: LAST / Resolution: 1.85→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2464 0 129 357 2950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222637
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2982.0183591
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8515327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52724.182110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09115399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9541519
X-RAY DIFFRACTIONr_chiral_restr0.0980.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022050
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.21418
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21851
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2830.2270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.2133
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3210.251
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8651.51671
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3322590
X-RAY DIFFRACTIONr_scbond_it2.65531173
X-RAY DIFFRACTIONr_scangle_it4.0134.51001
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 111 -
Rwork0.222 1984 -
obs--96.9 %

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