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- PDB-6yq8: Crystal structure of native Phycocyanin from T. elongatus in spac... -

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Basic information

Entry
Database: PDB / ID: 6yq8
TitleCrystal structure of native Phycocyanin from T. elongatus in spacegroup P63 at 1.8 Angstroms
Components(C-phycocyanin ...) x 2
KeywordsPHOTOSYNTHESIS / Native C-Phycocyanin / antenna protein / heterodimer / ligand-bound / Phycobilisome / Chromophore / ELECTRON TRANSPORT
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycocyanin, alpha subunit / Phycocyanin, beta subunit / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / TRIETHYLENE GLYCOL / C-phycocyanin alpha subunit / C-phycocyanin beta subunit
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsFeiler, C.G. / Falke, S. / Sarrou, I.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening.
Authors: Sarrou, I. / Feiler, C.G. / Falke, S. / Peard, N. / Yefanov, O. / Chapman, H.
History
DepositionApr 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)38,75119
Polymers35,6732
Non-polymers3,07817
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-36 kcal/mol
Surface area14670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.514, 153.514, 39.358
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

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C-phycocyanin ... , 2 types, 2 molecules AB

#1: Protein C-phycocyanin alpha chain


Mass: 17456.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / Gene: cpcA, tlr1958
Production host: Thermosynechococcus elongatus (strain BP-1) (bacteria)
References: UniProt: P50032
#2: Protein C-phycocyanin beta chain


Mass: 18216.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Residue 72: N4-methylasparagine; parent Asn
Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / References: UniProt: P50033

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Non-polymers , 5 types, 237 molecules

#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1% Nucleosides Mix, 0.1M Buffer System3, 50% Precipitant Mix 3, Morpheus Screen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.82→44.32 Å / Num. obs: 48140 / % possible obs: 99.96 % / Redundancy: 11.13 % / Biso Wilson estimate: 41.34 Å2 / Rrim(I) all: 0.06 / Net I/σ(I): 22.21
Reflection shellResolution: 1.82→1.94 Å / Mean I/σ(I) obs: 0.82 / Num. unique obs: 4751 / Rrim(I) all: 0.267 / % possible all: 99.81

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YPQ

6ypq


Resolution: 1.82→44.32 Å / SU ML: 0.2443 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.7206
RfactorNum. reflection% reflection
Rfree0.201 2100 4.36 %
Rwork0.1788 --
obs0.1798 48139 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 59.05 Å2
Refinement stepCycle: LAST / Resolution: 1.82→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 209 223 2931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01322773
X-RAY DIFFRACTIONf_angle_d1.31813748
X-RAY DIFFRACTIONf_chiral_restr0.0627407
X-RAY DIFFRACTIONf_plane_restr0.0069481
X-RAY DIFFRACTIONf_dihedral_angle_d15.9077450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.860.39091370.36513003X-RAY DIFFRACTION97.91
1.86-1.910.36271370.33353010X-RAY DIFFRACTION100
1.91-1.960.29851400.28633066X-RAY DIFFRACTION99.97
1.96-2.020.29721380.25363021X-RAY DIFFRACTION99.97
2.02-2.080.24161400.23093083X-RAY DIFFRACTION99.97
2.08-2.160.22971380.21313027X-RAY DIFFRACTION100
2.16-2.240.20891390.18633038X-RAY DIFFRACTION100
2.24-2.350.19551390.17943043X-RAY DIFFRACTION99.97
2.35-2.470.19791410.1733100X-RAY DIFFRACTION99.97
2.47-2.620.22751400.17963077X-RAY DIFFRACTION100
2.62-2.830.21371400.18883057X-RAY DIFFRACTION100
2.83-3.110.20241400.18493068X-RAY DIFFRACTION100
3.11-3.560.18421410.1783104X-RAY DIFFRACTION100
3.56-4.480.17331420.15223116X-RAY DIFFRACTION100
4.48-44.320.18961480.16183226X-RAY DIFFRACTION100
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)
13.33269345632-2.11292620050.5691790596964.82756292291-1.074256334541.285222365450.0580747439339-0.3123863883940.2462301396520.392308410162-0.1078862589770.24226059614-0.0522372213038-0.1660797788570.06090168083350.408486522034-0.1632622619640.01288792194150.585334620719-0.06614594037140.40150001391343.2642566175-50.153817879216.2263060956
22.16687641920.9749340017270.01814056437113.031212312910.1236294284822.293778041830.0760810017947-0.501795047761.005859320730.349831211953-0.1753920142071.02932708145-0.597280773883-0.4587651032050.05276291646520.5736609246880.05452312923680.0612293458840.600601746986-0.1705241220370.88524257671739.9305553883-24.317781876314.416731994
34.03406197286-0.4824539895820.01779696641792.15344183793-1.257894802242.345625312070.02812663628750.1296309107690.0289771870292-0.8092541894430.1538830335190.10388466339-0.00880541420427-0.1443699672250.06312018406670.536181670426-0.12949670104-0.035407679720.5169805672170.02331513231170.47647289525843.2956913407-40.54460727863.83894581706
42.03166238164-0.07740629018060.5743467466982.49268780138-3.272077612624.43022297229-0.177055984010.09766736069330.160208040261-0.9455646937080.3133522935361.20331248150.130917652656-0.633531372741-0.2416840725430.471332897219-0.0983654607171-0.112699907270.684204950248-0.01348703774710.56392578762733.904726435-49.13401420945.29888978278
54.42574099936-0.6154395495190.1567727825860.9226046969110.171771582410.4253997231410.007640572626860.2930406513270.0374032892013-0.105071566915-0.0342919226841-0.2293201228450.02948282387570.08229098892480.02944974866250.367595181615-0.132858171620.004193353134310.5741200692480.02994109569350.3628239637856.8058876719-65.64783300524.3474919292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 162 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 20 )
4X-RAY DIFFRACTION4chain 'B' and (resid 21 through 33 )
5X-RAY DIFFRACTION5chain 'B' and (resid 34 through 172 )

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