[English] 日本語
Yorodumi
- PDB-1lia: CRYSTAL STRUCTURE OF R-PHYCOERYTHRIN FROM POLYSIPHONIA AT 2.8 A R... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lia
TitleCRYSTAL STRUCTURE OF R-PHYCOERYTHRIN FROM POLYSIPHONIA AT 2.8 A RESOLUTION
Components(R-PHYCOERYTHRIN) x 2
KeywordsLIGHT HARVESTING PROTEIN
Function / homology
Function and homology information


: / : / phycobilisome / chloroplast thylakoid membrane / photosynthesis
Similarity search - Function
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 / PHYCOUROBILIN / R-phycoerythrin alpha chain / R-phycoerythrin beta chain / R-phycoerythrin alpha chain / R-phycoerythrin beta chain
Similarity search - Component
Biological speciesPolysiphonia urceolata (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsLiang, D.C. / Jiang, T. / Chang, W.R.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Crystal structure of R-phycoerythrin from Polysiphonia urceolata at 2.8 A resolution.
Authors: Chang, W.R. / Jiang, T. / Wan, Z.L. / Zhang, J.P. / Yang, Z.X. / Liang, D.C.
#1: Journal: Prog.Nat.Sci. / Year: 1995
Title: Crystal Structure of R-Phycoerythrin from Polysiphonia Urceolata at 0.5Nm Resolution
Authors: Chang, W.R. / Wan, Z.L. / Jiang, T. / Zhang, J.P. / Song, H.W. / Wang, S.G. / Gui, L.L. / Liang, D.C. / Zhu, J.C. / Yang, Z.X.
History
DepositionJan 29, 1996-
Revision 1.0Jul 29, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: R-PHYCOERYTHRIN
B: R-PHYCOERYTHRIN
K: R-PHYCOERYTHRIN
L: R-PHYCOERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,07614
Polymers73,1854
Non-polymers5,89110
Water2,414134
1
A: R-PHYCOERYTHRIN
B: R-PHYCOERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5387
Polymers36,5922
Non-polymers2,9455
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-89 kcal/mol
Surface area15730 Å2
MethodPISA
2
K: R-PHYCOERYTHRIN
L: R-PHYCOERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5387
Polymers36,5922
Non-polymers2,9455
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-84 kcal/mol
Surface area15700 Å2
MethodPISA
3
A: R-PHYCOERYTHRIN
B: R-PHYCOERYTHRIN
K: R-PHYCOERYTHRIN
L: R-PHYCOERYTHRIN
hetero molecules

A: R-PHYCOERYTHRIN
B: R-PHYCOERYTHRIN
K: R-PHYCOERYTHRIN
L: R-PHYCOERYTHRIN
hetero molecules

A: R-PHYCOERYTHRIN
B: R-PHYCOERYTHRIN
K: R-PHYCOERYTHRIN
L: R-PHYCOERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,22742
Polymers219,55412
Non-polymers17,67330
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area73310 Å2
ΔGint-590 kcal/mol
Surface area71300 Å2
MethodPISA
4
A: R-PHYCOERYTHRIN
B: R-PHYCOERYTHRIN
hetero molecules

A: R-PHYCOERYTHRIN
B: R-PHYCOERYTHRIN
hetero molecules

A: R-PHYCOERYTHRIN
B: R-PHYCOERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,61421
Polymers109,7776
Non-polymers8,83615
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 area29550 Å2
ΔGint-301 kcal/mol
Surface area42830 Å2
MethodPISA
5
K: R-PHYCOERYTHRIN
L: R-PHYCOERYTHRIN
hetero molecules

K: R-PHYCOERYTHRIN
L: R-PHYCOERYTHRIN
hetero molecules

K: R-PHYCOERYTHRIN
L: R-PHYCOERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,61421
Polymers109,7776
Non-polymers8,83615
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 area29420 Å2
ΔGint-285 kcal/mol
Surface area42800 Å2
MethodPISA
6


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20330 Å2
ΔGint-177 kcal/mol
Surface area27870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.800, 189.800, 60.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.63196, 0.775, -0.00107), (0.77494, 0.63194, 0.01112), (0.0093, 0.0062, -0.99994)0.13, -0.305, 46.21576
2given(-0.62986, 0.77667, 0.00775), (0.7767, 0.62985, 0.0047), (-0.00123, 0.00898, -0.99996)-0.23609, -0.10923, 46.34393

-
Components

#1: Protein R-PHYCOERYTHRIN


Mass: 17855.041 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Polysiphonia urceolata (eukaryote) / References: UniProt: Q01921, UniProt: P84861*PLUS
#2: Protein R-PHYCOERYTHRIN


Mass: 18737.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Polysiphonia urceolata (eukaryote) / References: UniProt: Q01922, UniProt: P84862*PLUS
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical ChemComp-PUB / PHYCOUROBILIN / Phycourobilin


Mass: 590.710 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H42N4O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE DIHEDRAL ANGLE OF B 77 AND L 77 IS UNUSUAL BUT THE SAME AS OTHER PHYCOBILIPROTINS.
Sequence detailsBECAUSE THE SEQUENCE OF R-PHYCOERYTHRIN FROM POLYSIPHONIA URCEOLATA IS UNKNOWN, THE AUTHORS USED ...BECAUSE THE SEQUENCE OF R-PHYCOERYTHRIN FROM POLYSIPHONIA URCEOLATA IS UNKNOWN, THE AUTHORS USED THE SEQUENCE OF R-PHYCOERYTHRIN FROM POLYSIPHONIA BOLDII FOR MODEL BUILDING. THE FOLLOWING SHOULD BE NOTED: RESIDUE NOTES LYS A 43 MAP IS WEAK THR A 136 LIKE ILE IN THE DENSITY MAP LYS B 15 MAP IS WEAK, LIKE ALA VAL B 173 LIKE ILE IN THE DENSITY MAP LYS K 43 MAP IS WEAK THR K 136 LIKE ILE IN THE DENSITY MAP LYS L 15 MAP IS WEAK, LIKE ALA VAL L 173 LIKE ILE IN THE DENSITY MAP

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 40 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.05 Msodium phosphate1drop
23 %(w/v)ammonium sulfate1dropor PEG6000
310 mg/mlprotein1drop
40.05 Msodium phosphate1reservoir
58 %ammonium sulfate1reservoir
63 %(w/v)1reservoirNaCl

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS-NICOLET X200B / Detector: AREA DETECTOR / Date: Mar 15, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.73→25 Å / Num. obs: 21280 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.042

-
Processing

Software
NameClassification
XENGENdata collection
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
X-PLORphasing
RefinementResolution: 2.8→10 Å / σ(F): 4
RfactorNum. reflection% reflection
Rfree0.182 -10 %
Rwork0.18 --
obs0.18 17513 90 %
Displacement parametersBiso mean: 12 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5112 0 430 134 5676
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg3.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.78
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.09
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19.PRO
X-RAY DIFFRACTION2RPECHROMO.PARRPECHROMO.TOP
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.78
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.09

+
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