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- PDB-5ook: Structure of A. marina Phycocyanin contains overlapping isoforms -

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Basic information

Entry
Database: PDB / ID: 5ook
TitleStructure of A. marina Phycocyanin contains overlapping isoforms
Components
  • Phycocyanin, alpha subunit
  • Phycocyanin, beta subunit
KeywordsPHOTOSYNTHESIS / Models / Phycobilisome / Phycocyanin / A. marina
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 / DI(HYDROXYETHYL)ETHER / Phycocyanin, alpha subunit / Phycocyanin, beta subunit
Similarity search - Component
Biological speciesAcaryochloris marina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBar-Zvi, S. / Lahav, A. / Blankenship, E.R. / Adir, N.
Funding support Israel, 1items
OrganizationGrant numberCountry
United States - Israel Binational Science Foundation (BSF)2014395 Israel
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: Structural heterogeneity leads to functional homogeneity in A. marina phycocyanin.
Authors: Bar-Zvi, S. / Lahav, A. / Harris, D. / Niedzwiedzki, D.M. / Blankenship, R.E. / Adir, N.
History
DepositionAug 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2024Group: 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: Phycocyanin, alpha subunit
B: Phycocyanin, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,25615
Polymers35,4292
Non-polymers2,82713
Water99155
1
A: Phycocyanin, alpha subunit
B: Phycocyanin, beta subunit
hetero molecules

A: Phycocyanin, alpha subunit
B: Phycocyanin, beta subunit
hetero molecules

A: Phycocyanin, alpha subunit
B: Phycocyanin, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,76845
Polymers106,2866
Non-polymers8,48239
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_685-y+1,x-y+3,z1
crystal symmetry operation3_365-x+y-2,-x+1,z1
Buried area31350 Å2
ΔGint-191 kcal/mol
Surface area40780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.806, 152.806, 39.312
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Phycocyanin, alpha subunit /


Mass: 17390.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina (bacteria) / References: UniProt: A8ZMJ4
#2: Protein Phycocyanin, beta subunit /


Mass: 18038.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acaryochloris marina (bacteria) / References: UniProt: A8ZMJ5
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.31 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M HEPES pH 6.5, 0.1M MgCl2, 9% PEG 2K

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→132.33 Å / Num. obs: 31134 / % possible obs: 99.9 % / Redundancy: 9.7 % / Biso Wilson estimate: 38.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.033 / Net I/σ(I): 10.6
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3105 / CC1/2: 0.92 / Rpim(I) all: 0.255 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0171refinement
PHENIX1.9_1692refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CPC

1cpc


Resolution: 2.1→132.33 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 9.551 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.14 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21517 1474 4.7 %RANDOM
Rwork0.19307 ---
obs0.19418 29647 99.85 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 59.807 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å2-0 Å2
3----0.77 Å2
Refinement stepCycle: 1 / Resolution: 2.1→132.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 199 55 2735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022734
X-RAY DIFFRACTIONr_bond_other_d0.0030.022547
X-RAY DIFFRACTIONr_angle_refined_deg2.2362.0343676
X-RAY DIFFRACTIONr_angle_other_deg1.0983.0015875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6665331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28924.444108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91715404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0151516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023020
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02536
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7822.0361333
X-RAY DIFFRACTIONr_mcbond_other0.782.0351332
X-RAY DIFFRACTIONr_mcangle_it1.2483.0451658
X-RAY DIFFRACTIONr_mcangle_other1.2483.0461659
X-RAY DIFFRACTIONr_scbond_it2.0292.751401
X-RAY DIFFRACTIONr_scbond_other2.0282.751401
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5513.8842018
X-RAY DIFFRACTIONr_long_range_B_refined6.01526.5873127
X-RAY DIFFRACTIONr_long_range_B_other6.01426.6123128
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 96 -
Rwork0.278 2195 -
obs--99.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8872.730.68282.76620.7531.087-0.17870.3766-0.6977-0.32830.3979-0.96350.1620.7299-0.21920.48350.10850.21470.5097-0.04360.7531-123.387152.218-10.496
21.6303-1.1020.17873.92810.05161.0641-0.068-0.11060.22960.10240.04530.00250.0748-0.0280.02260.41380.0027-0.0040.0637-0.0040.0433-155.614147.695-0.511
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 174
2X-RAY DIFFRACTION2B1 - 174

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