[English] 日本語
Yorodumi
- PDB-5nb3: High resolution C-phycoerythrin from marine cyanobacterium Phormi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5nb3
TitleHigh resolution C-phycoerythrin from marine cyanobacterium Phormidium sp. A09DM at pH 7.5
Components(Phycoerythrin ...) x 2
KeywordsPHOTOSYNTHESIS / marine cyanobacterium Phormidium sp.A09DM / C-phycoerythrin / pigment-protein light harvesting complex
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived 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
FORMIC ACID / PHYCOERYTHROBILIN / Phycoerythrin Alpha subunit / Phycoerythrin Beta subunit
Similarity search - Component
Biological speciesPhormidium rubidum A09DM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.38 Å
AuthorsSonani, R.R. / Roszak, A.W. / Ortmann de Percin Northumberland, C. / Madamwar, D. / Cogdell, R.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0001035 United States
CitationJournal: Photosyn. Res. / Year: 2018
Title: An improved crystal structure of C-phycoerythrin from the marine cyanobacterium Phormidium sp. A09DM.
Authors: Sonani, R.R. / Roszak, A.W. / Ortmann de Percin Northumberland, C. / Madamwar, D. / Cogdell, R.J.
History
DepositionMar 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.3Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 1, 2025Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
B: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
C: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
D: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
E: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
F: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
G: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
H: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
I: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
J: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
K: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
L: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
M: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
N: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
O: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
P: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
Q: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
R: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
S: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
T: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
U: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
V: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
W: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
X: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)482,688138
Polymers444,37224
Non-polymers38,316114
Water140,4997799
1
A: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
B: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
C: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
D: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
E: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
F: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
M: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
N: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
O: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
P: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
Q: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
R: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,35670
Polymers222,18612
Non-polymers19,16958
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80300 Å2
ΔGint-815 kcal/mol
Surface area71860 Å2
MethodPISA
2
G: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
H: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
I: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
J: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
K: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
L: Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit
S: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
T: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
U: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
V: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
W: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
X: Phycoerythrin Beta subunit,Phycoerythrin Beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,33368
Polymers222,18612
Non-polymers19,14756
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80120 Å2
ΔGint-750 kcal/mol
Surface area71900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.046, 110.170, 118.516
Angle α, β, γ (deg.)78.76, 82.28, 60.43
Int Tables number1
Space group name H-MP1

-
Components

-
Phycoerythrin ... , 2 types, 24 molecules ABCDEFGHIJKLMNOPQRSTUVWX

#1: Protein
Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit,Phycoerythrin Alpha subunit


Mass: 17660.830 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Details: Two PEB chromophores are covalently linked by residues Cys82 (PEB166) and Cys139 (PEB167)
Source: (natural) Phormidium rubidum A09DM (bacteria) / References: UniProt: A0A0E3W010
#2: Protein
Phycoerythrin Beta subunit,Phycoerythrin Beta subunit


Mass: 19370.189 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Details: Three PEB chromophores are link covalently to Cys80 (PEB186), Cys165 (PEB187), and Cys48/Cys59 (PEB188)
Source: (natural) Phormidium rubidum A09DM (bacteria) / References: UniProt: A0A0E4G455

-
Non-polymers , 7 types, 7913 molecules

#3: Chemical...
ChemComp-PEB / PHYCOERYTHROBILIN


Mass: 588.694 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7799 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Morpheus screen condition G8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.38→95.42 Å / Num. obs: 932250 / % possible obs: 95.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 8.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.077 / Net I/σ(I): 7.3
Reflection shellResolution: 1.38→1.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 67249 / CC1/2: 0.477 / Rpim(I) all: 0.801 / % possible all: 93.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5aqd

5aqd


Resolution: 1.38→95.42 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.694 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 46444 5 %RANDOM
Rwork0.155 ---
obs0.158 878170 94.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20.08 Å20.27 Å2
2---0.18 Å2-0.36 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.38→95.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31032 0 2762 7799 41593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01936163
X-RAY DIFFRACTIONr_bond_other_d0.0030.0233826
X-RAY DIFFRACTIONr_angle_refined_deg2.5962.05349531
X-RAY DIFFRACTIONr_angle_other_deg1.284378201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.11954665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36423.7091402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.717155670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.13815294
X-RAY DIFFRACTIONr_chiral_restr0.1120.25434
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0241583
X-RAY DIFFRACTIONr_gen_planes_other0.0170.027579
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6211.20817481
X-RAY DIFFRACTIONr_mcbond_other1.6211.20817482
X-RAY DIFFRACTIONr_mcangle_it1.9771.8221988
X-RAY DIFFRACTIONr_mcangle_other1.9771.8221989
X-RAY DIFFRACTIONr_scbond_it2.2211.45418682
X-RAY DIFFRACTIONr_scbond_other2.2161.45318653
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6552.09227348
X-RAY DIFFRACTIONr_long_range_B_refined5.75718.57944229
X-RAY DIFFRACTIONr_long_range_B_other3.61515.66341232
X-RAY DIFFRACTIONr_rigid_bond_restr3.107369989
X-RAY DIFFRACTIONr_sphericity_free36.74654882
X-RAY DIFFRACTIONr_sphericity_bonded10.923572125
LS refinement shellResolution: 1.38→1.42 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 3198 -
Rwork0.357 61904 -
obs--90.16 %

+
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