[English] 日本語
Yorodumi
- PDB-1eyx: CRYSTAL STRUCTURE OF R-PHYCOERYTHRIN AT 2.2 ANGSTROMS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1eyx
TitleCRYSTAL STRUCTURE OF R-PHYCOERYTHRIN AT 2.2 ANGSTROMS
Components(R-PHYCOERYTHRIN) x 3
KeywordsPHOTOSYNTHESIS / R-PHYCOERYTHRIN / MACROSEEDING / TWIN / PROTEIN STRUCTURE / SEQUENCES / PHYCOBILIPROTEIN / RED ALGAE
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 beta chain / R-phycoerythrin alpha chain
Similarity search - Component
Biological speciesGracilaria chilensis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsContreras-Martel, C. / Legrand, P. / Piras, C. / Vernede, X. / Martinez-Oyanedel, J. / Bunster, M. / Fontecilla-Camps, J.C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and 2.2 A resolution structure of R-phycoerythrin from Gracilaria chilensis: a case of perfect hemihedral twinning.
Authors: Contreras-Martel, C. / Martinez-Oyanedel, J. / Bunster, M. / Legrand, P. / Piras, C. / Vernede, X. / Fontecilla-Camps, J.C.
History
DepositionMay 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Mar 12, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,10718
Polymers74,0236
Non-polymers6,08312
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21680 Å2
ΔGint-204 kcal/mol
Surface area28020 Å2
MethodPISA
2
A: R-PHYCOERYTHRIN
B: R-PHYCOERYTHRIN
K: R-PHYCOERYTHRIN
L: R-PHYCOERYTHRIN
G: R-PHYCOERYTHRIN
H: R-PHYCOERYTHRIN
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)240,32054
Polymers222,07018
Non-polymers18,24936
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area77450 Å2
ΔGint-668 kcal/mol
Surface area71640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.268, 187.268, 59.109
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

-
Protein , 2 types, 4 molecules AKBL

#1: Protein R-PHYCOERYTHRIN


Mass: 17770.857 Da / Num. of mol.: 2 / Fragment: ALPHA CHAIN / Source method: isolated from a natural source / Source: (natural) Gracilaria chilensis (eukaryote) / Organelle: CHLOROPLAST / References: UniProt: Q7SIG0
#2: Protein R-PHYCOERYTHRIN


Mass: 18634.182 Da / Num. of mol.: 2 / Fragment: BETA CHAIN / Source method: isolated from a natural source / Source: (natural) Gracilaria chilensis (eukaryote) / Organelle: CHLOROPLAST / References: UniProt: Q7SIF9

-
Protein/peptide , 1 types, 2 molecules GH

#3: Protein/peptide R-PHYCOERYTHRIN


Mass: 606.694 Da / Num. of mol.: 2 / Fragment: GAMMA CHAIN / Source method: isolated from a natural source / Source: (natural) Gracilaria chilensis (eukaryote) / Organelle: CHLOROPLAST

-
Non-polymers , 4 types, 122 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


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


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


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.7 %
Description: A PERFECT HEMIHEDRAL TWINNED CRYSTAL. STANLEY DISTRIBUTION, 1.44. TWIN FRACTION, 0.48.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200 MM HEPES, 500 MM SODIUM CHLORIDE, 50 MM POTASIUM CHLORIDE, 15 MM SODIUM AZIDE, 16% AMMONIUM SULPHATE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 294 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112-15 mg/mlprotein1drop
216-18 %satammonium sulfate1reservoir
3200 mMHEPES1reservoir
4500 mMsodium chloride1reservoir
515 mMsodium azide1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9783
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 31, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9783 Å / Relative weight: 1
ReflectionResolution: 2.16→42.55 Å / Num. obs: 38751 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 7.3
Reflection shellResolution: 2.16→2.28 Å / Redundancy: 2 % / Rmerge(I) obs: 0.039 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.039 / % possible all: 89.4
Reflection
*PLUS
Num. measured all: 123143
Reflection shell
*PLUS
% possible obs: 89.4 %

-
Processing

Software
NameVersionClassification
AMoREphasing
SHELXL-97refinement
XDSV. 1998data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LIA

1lia


Resolution: 2.25→999 Å / Num. parameters: 2290 / Num. restraintsaints: 3005 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1856 5.3 %RANDOM BY LAYERS
all0.18 34796 --
obs0.192 -94.6 %-
Refine analyzeOccupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5654
Refinement stepCycle: LAST / Resolution: 2.25→999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5169 0 440 110 5719
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.012
X-RAY DIFFRACTIONs_similar_dist0.023
X-RAY DIFFRACTIONs_from_restr_planes0.016
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.006
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.018
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.091
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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