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

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Basic information

Entry
Database: PDB / ID: 6ypq
TitleCrystal structure of native Phycocyanin from T. elongatus in spacegroup R32 at 1.29 Angstroms
Components(C-phycocyanin ...) x 2
KeywordsELECTRON TRANSPORT / Native C-Phycocyanin / Antenna protein / light harvesting
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 / GLYCINE / LYSINE / C-phycocyanin alpha subunit / C-phycocyanin beta subunit
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 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.year / _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)37,8098
Polymers35,6732
Non-polymers2,1366
Water7,494416
1
A: C-phycocyanin alpha chain
B: C-phycocyanin beta chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)226,85348
Polymers214,04012
Non-polymers12,81336
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 area61840 Å2
ΔGint-514 kcal/mol
Surface area66930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.169, 187.169, 59.927
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-603-

HOH

21A-647-

HOH

31A-784-

HOH

41B-392-

HOH

51B-463-

HOH

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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 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 genetically manipulated source
Details: modified residue 72: N4-methylasparagine
Source: (gene. exp.) Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1 / Gene: cpcB, tlr1957
Production host: Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: P50033

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Non-polymers , 4 types, 422 molecules

#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Chemical ChemComp-LYS / LYSINE / Lysine


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 416 / 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

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus: 0,1M Amino acids, 0,1M Buffer System 1, 30%v/v P500MME_P20K
PH range: 6.5

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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: 1.29→48.19 Å / Num. obs: 99233 / % possible obs: 99.1 % / Redundancy: 9 % / Biso Wilson estimate: 14.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.012 / Rrim(I) all: 0.037 / Net I/σ(I): 30.3
Reflection shellResolution: 1.29→1.31 Å / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 4327 / CC1/2: 0.945 / Rpim(I) all: 0.19 / Rrim(I) all: 0.453 / % possible all: 87.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JBO

1jbo


Resolution: 1.29→46.79 Å / SU ML: 0.1249 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8619
RfactorNum. reflection% reflection
Rfree0.1701 1691 1.7 %
Rwork0.1526 --
obs0.1529 99198 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.55 Å2
Refinement stepCycle: LAST / Resolution: 1.29→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 0 154 418 3070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00782795
X-RAY DIFFRACTIONf_angle_d1.20283808
X-RAY DIFFRACTIONf_chiral_restr0.0583414
X-RAY DIFFRACTIONf_plane_restr0.0057498
X-RAY DIFFRACTIONf_dihedral_angle_d16.43651045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.330.27661270.24477368X-RAY DIFFRACTION90.13
1.33-1.370.23561410.20558092X-RAY DIFFRACTION99.18
1.37-1.420.21071410.18898155X-RAY DIFFRACTION99.95
1.42-1.480.19181420.17128170X-RAY DIFFRACTION99.92
1.48-1.540.19991420.15488156X-RAY DIFFRACTION99.92
1.54-1.630.1561410.1498157X-RAY DIFFRACTION99.98
1.63-1.730.18011420.14658186X-RAY DIFFRACTION99.98
1.73-1.860.15861420.14838203X-RAY DIFFRACTION99.98
1.86-2.050.17141420.14838188X-RAY DIFFRACTION100
2.05-2.340.15811420.14178217X-RAY DIFFRACTION99.99
2.34-2.950.1511430.14648244X-RAY DIFFRACTION99.99
2.95-46.790.17151460.15038371X-RAY DIFFRACTION99.96
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)
13.96945575909-1.855805137540.01500573605612.14371140663-0.5115781662471.931614262390.0191315254668-0.04137251686350.5520898010290.0755620441046-0.125035206015-0.0149491047294-0.0832910570169-0.03398170750780.1131236829830.1449520001220.0154132483377-0.01095570771390.190059276763-0.02792504200750.365337349411-9.81234107908-23.648804959-5.29325190844
21.89494137373-0.8493120425270.5306876313350.380478469472-0.251570916810.137280072160.05323029069390.0181186518748-0.26645117696-0.0395210569167-0.004562461668270.08248847986160.05207576583060.0813020084772-0.04496023939350.1115509749730.00820033179402-0.003456662279050.133261663777-0.0176847601140.306168225693-34.4919805606-25.6151692918-6.79593073706
30.5919334487640.56516273798-2.052446669241.47697324812-1.389510621287.507410398090.0322261485368-0.1026254622570.263723230147-0.0367261438437-0.01066547029390.249409242338-0.213248543047-0.13023366718-0.0107692339220.1164822820910.0170580160441-0.0216265702620.105906801656-0.02193986345850.302550052441-50.027840253-0.130353038939-7.61032782029
41.02154657238-0.4209469986880.1148320231691.20710271794-0.1282537971210.4696919554280.00777929487102-0.00161984448783-0.0779120180637-0.006368868877830.0114981423304-0.0208338476825-0.01028311255510.0620182274283-0.01677542262650.082498199466-0.00411058999881-0.004671183937180.103248760091-0.02194770842440.218059648577-36.0440146068-14.1000488928-6.07660719533
56.028525485580.445259624208-3.441184154120.8615831396-2.198282131966.523398748161.009071392340.7602241357240.564928543439-0.940958220138-0.454684685925-1.17608990250.1123501432960.0565970350113-0.5868498727850.3018408394160.0352182676324-0.006007441667340.755558170087-0.3873324943040.627712024106-22.0576682758-17.6389132692.2537658572
63.2758506468-1.242075369881.397845255241.72681846868-1.128141030891.105196210160.1034075140480.3729594919760.0177070833818-0.17926311512-0.188215766811-0.269168257750.1086541543480.3517670125590.05557778237710.1263049558390.0368073126232-0.002551346593520.200045324124-0.03913547704060.262792405398-26.3302962816-21.6641135326-18.573664717
74.66173590854-5.238287348382.438739318565.93849755327-2.444845944722.978780643490.4910857118020.317532781481-0.396335662907-0.539479541836-0.221294799657-0.08714641567450.05448184859720.203759513644-0.1709261768070.20933332460.0744722306144-0.04601427392630.238119989303-0.1320397619170.426666356452-27.6164013325-34.360856553-17.0307380046
82.603813687970.164467456836-0.3485392315491.05778022931-0.07394368958010.41421032209-0.01694800444410.279394457767-0.104202540428-0.065559855609-0.03969436590540.00272689926133-0.021095268210.0010003580390.05781947363490.09788217706230.0232411427494-0.01631942088360.181735162023-0.01227307090810.1812877092417.52886693039-32.5309081286-16.5176850696
99.126288096661.00063433819-0.2826166613740.5026519395880.1682426492140.09394472573540.09654533833680.3052393187710.3826325596320.00293492935294-0.04168680491990.0766674195494-0.0736021576156-0.0521079813282-0.05812810491290.1271603651540.03460900268860.01239489502230.1923094078110.0472225319420.2469394121063.61851681103-25.1539887009-13.5799676397
103.075688423930.38150545707-0.4536147377560.666275715061-0.2491538498610.6695032068890.1293007297080.6739559679140.408153317372-0.106675311922-0.03999154050760.155225526309-0.123169137759-0.0452572779081-0.08127210774960.1607543780250.05876514555610.008573514256470.3513752661590.07336572250240.2653568624750.433484245419-24.260637434-21.6070063248
111.5544023781-0.1169135844740.2286920324455.27659305007-2.068002116782.160939093430.0679561880150.589551659426-0.327901535122-0.348512439224-0.1690395042610.03138210275210.1738014828610.09044353215460.1255990572330.1404362907220.0717818097871-0.03905444171190.314133229561-0.09058450830960.280463040574-7.31359366625-37.6452557255-20.0010200733
128.62812627139-5.505518743293.352358691426.1356026816-1.426007278286.91005164364-0.272516642620.990488797795-0.315427085566-1.37564171354-0.118563136989-0.238182543205-0.8312445138621.676136778160.4368800743130.601536618831-0.0952274242079-0.1544179765470.505985600546-0.1558584284950.388939631557-38.1028432573-23.2425909565-22.1783578777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 62 )
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 77 )
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 174 )
5X-RAY DIFFRACTION5chain 'A' and (resid 601 through 701 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 20 )
7X-RAY DIFFRACTION7chain 'B' and (resid 21 through 33 )
8X-RAY DIFFRACTION8chain 'B' and (resid 34 through 77 )
9X-RAY DIFFRACTION9chain 'B' and (resid 78 through 101 )
10X-RAY DIFFRACTION10chain 'B' and (resid 102 through 144 )
11X-RAY DIFFRACTION11chain 'B' and (resid 145 through 174 )
12X-RAY DIFFRACTION12chain 'B' and (resid 601 through 601 )

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