[English] 日本語
Yorodumi
- PDB-1phn: STRUCTURE OF PHYCOCYANIN FROM CYANIDIUM CALDARIUM AT 1.65A RESOLUTION -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1phn
TitleSTRUCTURE OF PHYCOCYANIN FROM CYANIDIUM CALDARIUM AT 1.65A RESOLUTION
Components(PHYCOCYANIN) x 2
KeywordsELECTRON TRANSPORT / PHYCOCYANIN / PHYCOBILISOME
Function / homology
Function and homology information


phycobilisome / chloroplast 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 / PHYCOERYTHROBILIN / C-phycocyanin alpha chain / C-phycocyanin beta chain
Similarity search - Component
Biological speciesCyanidium caldarium (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsStec, B. / Troxler, R.F. / Teeter, M.M.
CitationJournal: Biophys.J. / Year: 1999
Title: Crystal structure of C-phycocyanin from Cyanidium caldarium provides a new perspective on phycobilisome assembly.
Authors: Stec, B. / Troxler, R.F. / Teeter, M.M.
History
DepositionJun 21, 1995Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHYCOCYANIN
B: PHYCOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5685
Polymers35,8022
Non-polymers1,7663
Water10,305572
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-65 kcal/mol
Surface area15040 Å2
MethodPISA
2
A: PHYCOCYANIN
B: PHYCOCYANIN
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)225,41030
Polymers214,81412
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 area60220 Å2
ΔGint-481 kcal/mol
Surface area68720 Å2
MethodPISA
3
A: PHYCOCYANIN
B: PHYCOCYANIN
hetero molecules

A: PHYCOCYANIN
B: PHYCOCYANIN
hetero molecules

A: PHYCOCYANIN
B: PHYCOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,70515
Polymers107,4076
Non-polymers5,2989
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area24300 Å2
ΔGint-229 kcal/mol
Surface area40180 Å2
MethodPISA
4
B: PHYCOCYANIN
hetero molecules

B: PHYCOCYANIN
hetero molecules

A: PHYCOCYANIN
hetero molecules

A: PHYCOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,13710
Polymers71,6054
Non-polymers3,5326
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
Buried area11790 Å2
ΔGint-101 kcal/mol
Surface area31190 Å2
MethodPISA
5
A: PHYCOCYANIN
B: PHYCOCYANIN
hetero molecules

A: PHYCOCYANIN
B: PHYCOCYANIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,13710
Polymers71,6054
Non-polymers3,5326
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area15670 Å2
ΔGint-132 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.420, 106.420, 176.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein PHYCOCYANIN


Mass: 17519.588 Da / Num. of mol.: 1
Fragment: CHAIN A IS THE ALPHA CHAIN, CHAIN B IS THE BETA CHAIN
Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: P00306
#2: Protein PHYCOCYANIN


Mass: 18282.729 Da / Num. of mol.: 1
Fragment: CHAIN A IS THE ALPHA CHAIN, CHAIN B IS THE BETA CHAIN
Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: P00311
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical ChemComp-PEB / PHYCOERYTHROBILIN


Mass: 588.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H40N4O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHIS STRUCTURE CONTAINS THREE PHYCOCYANOBILIN CHROMOPHORES ATTACHED BY THIOETHER BONDS TO CYSTEINES ...THIS STRUCTURE CONTAINS THREE PHYCOCYANOBILIN CHROMOPHORES ATTACHED BY THIOETHER BONDS TO CYSTEINES A 82, B 84, B 155.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
250 mMphosphate1drop
30.45 Mammonium sulfate1drop
40.02 %sodium azide1drop
51.0 Mammonium sulfate1reservoir

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→37 Å / Num. obs: 44677 / % possible obs: 95.6 % / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Rmerge(I) obs: 0.089
Reflection
*PLUS
% possible obs: 90.3 % / Redundancy: 3.3 %
Reflection shell
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 1.68 Å / % possible obs: 65 %

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
X-PLORphasing
RefinementResolution: 1.65→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.272 -18 %
Rwork0.183 --
obs0.183 43637 -
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2503 0 130 572 3205
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 12.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.81
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_deg1.79

+
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