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- PDB-4n6s: Crystals of cross-linked stabilized and functional Phycobilisomes... -

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Basic information

Entry
Database: PDB / ID: 4n6s
TitleCrystals of cross-linked stabilized and functional Phycobilisomes: only phycocyanin rods contribute to diffraction.
Components
  • C-phycocyanin alpha subunit
  • C-phycocyanin beta subunit
KeywordsPHOTOSYNTHESIS / antenna / glutaraldehyde cross-links / membrane associated
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 beta subunit / C-phycocyanin alpha subunit
Similarity search - Component
Biological speciesThermosynechococcus vulcanus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDavid, L. / Prado, M. / Arteni, A. / Elmlund, D.A. / Blankenship, R.E. / Adir, N.
CitationJournal: Biochim.Biophys.Acta / Year: 2014
Title: Structural studies show energy transfer within stabilized phycobilisomes independent of the mode of rod-core assembly.
Authors: David, L. / Prado, M. / Arteni, A.A. / Elmlund, D.A. / Blankenship, R.E. / Adir, N.
History
DepositionOct 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Sep 20, 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: C-phycocyanin alpha subunit
B: C-phycocyanin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4535
Polymers35,6872
Non-polymers1,7663
Water1,982110
1
A: C-phycocyanin alpha subunit
B: C-phycocyanin beta subunit
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)224,72030
Polymers214,12412
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 area60450 Å2
ΔGint-499 kcal/mol
Surface area69460 Å2
MethodPISA
2
A: C-phycocyanin alpha subunit
B: C-phycocyanin beta subunit
hetero molecules

A: C-phycocyanin alpha subunit
B: C-phycocyanin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,90710
Polymers71,3754
Non-polymers3,5326
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area16180 Å2
ΔGint-140 kcal/mol
Surface area27120 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-68 kcal/mol
Surface area15140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.070, 188.070, 60.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein C-phycocyanin alpha subunit


Mass: 17470.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: Q9AM02
#2: Protein C-phycocyanin beta subunit


Mass: 18216.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / References: UniProt: Q71RW8
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


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


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10-15 mg/ml phycobilisome in 0.9M phosphate buffer against a resevoir of 1.2-1.4M phosphate buffer. , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→54.3 Å / Num. obs: 16012 / % possible obs: 99.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 20
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 6.3 / Num. unique all: 2307 / % possible all: 98.4

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Processing

Software
NameClassification
DNAdata collection
PHASERphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O18

3o18


Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 807 -Random
Rwork0.192 ---
all-16005 --
obs-15198 99.9 %-
Displacement parametersBiso mean: 31.13 Å2
Refine analyzeLuzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.284 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2500 0 129 110 2739
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.2

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