[English] 日本語
Yorodumi
- PDB-6ypq: Crystal structure of native Phycocyanin from T. elongatus in spac... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 4 types, 422 molecules

#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN


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


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


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


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more