[English] 日本語
Yorodumi
- PDB-8b4n: X-ray structure of phycoerythrin from Porphyridium cruentum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b4n
TitleX-ray structure of phycoerythrin from Porphyridium cruentum
Components(B-phycoerythrin ...) x 2
KeywordsPHOTOSYNTHESIS / Microalgae / chromophore / red algae / Porphyridium cruentum
Function / homology
Function and homology information


phycobilisome / chloroplast thylakoid membrane / photosynthesis
Similarity search - Function
Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
N-METHYL ASPARAGINE / PHYCOERYTHROBILIN / B-phycoerythrin alpha chain / B-phycoerythrin beta chain
Similarity search - Component
Biological speciesPorphyridium purpureum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMerlino, A. / Ferraro, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Sustain Chem Eng / Year: 2023
Title: Inside out Porphyridium cruentum : Beyond the Conventional Biorefinery Concept.
Authors: Liberti, D. / Imbimbo, P. / Giustino, E. / D'Elia, L. / Ferraro, G. / Casillo, A. / Illiano, A. / Pinto, G. / Di Meo, M.C. / Alvarez-Rivera, G. / Corsaro, M.M. / Amoresano, A. / Zarrelli, A. ...Authors: Liberti, D. / Imbimbo, P. / Giustino, E. / D'Elia, L. / Ferraro, G. / Casillo, A. / Illiano, A. / Pinto, G. / Di Meo, M.C. / Alvarez-Rivera, G. / Corsaro, M.M. / Amoresano, A. / Zarrelli, A. / Ibanez, E. / Merlino, A. / Monti, D.M.
History
DepositionSep 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: B-phycoerythrin alpha chain
BBB: B-phycoerythrin beta chain
BbB: B-phycoerythrin beta chain
CCC: B-phycoerythrin alpha chain
DDD: B-phycoerythrin beta chain
DbD: B-phycoerythrin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,30020
Polymers109,9296
Non-polymers6,37114
Water5,837324
1
AAA: B-phycoerythrin alpha chain
BBB: B-phycoerythrin beta chain
BbB: B-phycoerythrin beta chain
CCC: B-phycoerythrin alpha chain
DDD: B-phycoerythrin beta chain
DbD: B-phycoerythrin beta chain
hetero molecules

AAA: B-phycoerythrin alpha chain
BBB: B-phycoerythrin beta chain
BbB: B-phycoerythrin beta chain
CCC: B-phycoerythrin alpha chain
DDD: B-phycoerythrin beta chain
DbD: B-phycoerythrin beta chain
hetero molecules

AAA: B-phycoerythrin alpha chain
BBB: B-phycoerythrin beta chain
BbB: B-phycoerythrin beta chain
CCC: B-phycoerythrin alpha chain
DDD: B-phycoerythrin beta chain
DbD: B-phycoerythrin beta chain
hetero molecules


  • defined by author&software
  • 349 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)348,90060
Polymers329,78618
Non-polymers19,11442
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area96660 Å2
ΔGint-871 kcal/mol
Surface area66050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.590, 186.590, 59.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

-
Components

-
B-phycoerythrin ... , 2 types, 6 molecules AAACCCBBBBbBDDDDbD

#1: Protein B-phycoerythrin alpha chain


Mass: 17824.029 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: P11392
#2: Protein
B-phycoerythrin beta chain


Mass: 18570.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Porphyridium purpureum (eukaryote) / References: UniProt: P11393

-
Non-polymers , 4 types, 338 molecules

#3: Chemical
ChemComp-PEB / PHYCOERYTHROBILIN / Phycoerythrobilin


Mass: 588.694 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MEN / N-METHYL ASPARAGINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10N2O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PE crystals were grown by hanging drop vapor diffusion method (Russo Krauss et al., 2013) using a drop containing 10 mg/mL PE in 0.250 M ammonium sulphate, 25.0 mM potassium phosphate at pH ...Details: PE crystals were grown by hanging drop vapor diffusion method (Russo Krauss et al., 2013) using a drop containing 10 mg/mL PE in 0.250 M ammonium sulphate, 25.0 mM potassium phosphate at pH 5.0, equilibrated with a reservoir containing 0.500 M ammonium sulphate, 50.0 mM potassium phosphate at pH 5.0.
PH range: 5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.597→46.648 Å / Num. obs: 100909 / % possible obs: 99 % / Redundancy: 9.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.035 / Rrim(I) all: 0.107 / Net I/σ(I): 12.9
Reflection shellResolution: 1.597→1.625 Å / Redundancy: 9 % / Rmerge(I) obs: 1.028 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 44973 / CC1/2: 0.595 / Rpim(I) all: 0.36 / Rrim(I) all: 0.999 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V58

3v58


Resolution: 1.6→46.648 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.264 / SU ML: 0.08 / Cross valid method: FREE R-VALUE / ESU R: 0.105 / ESU R Free: 0.105
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2564 4971 4.951 %
Rwork0.2217 95441 -
all0.223 --
obs-100412 98.994 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.932 Å2
Baniso -1Baniso -2Baniso -3
1--0.061 Å2-0.031 Å2-0 Å2
2---0.061 Å20 Å2
3---0.199 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5070 0 458 324 5852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135778
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155416
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.6547891
X-RAY DIFFRACTIONr_angle_other_deg1.4771.58512394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8215704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.98319.036332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.45715865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8931543
X-RAY DIFFRACTIONr_chiral_restr0.0880.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026942
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021315
X-RAY DIFFRACTIONr_nbd_refined0.2840.21444
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.25215
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22796
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22501
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2302
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1640.225
X-RAY DIFFRACTIONr_nbd_other0.1740.2114
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.217
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2380.21
X-RAY DIFFRACTIONr_mcbond_it1.8622.3822777
X-RAY DIFFRACTIONr_mcbond_other1.8612.3812776
X-RAY DIFFRACTIONr_mcangle_it2.4393.5723476
X-RAY DIFFRACTIONr_mcangle_other2.4393.5733477
X-RAY DIFFRACTIONr_scbond_it2.3872.6323001
X-RAY DIFFRACTIONr_scbond_other2.3772.6292996
X-RAY DIFFRACTIONr_scangle_it3.3733.8644409
X-RAY DIFFRACTIONr_scangle_other3.3683.864404
X-RAY DIFFRACTIONr_lrange_it4.1829.5196667
X-RAY DIFFRACTIONr_lrange_other4.14329.386615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6420.313640.2676986X-RAY DIFFRACTION97.9347
1.642-1.6870.3013560.2616852X-RAY DIFFRACTION98.1883
1.687-1.7350.2993480.2556614X-RAY DIFFRACTION98.3333
1.735-1.7890.3033350.2396471X-RAY DIFFRACTION98.4237
1.789-1.8470.2753170.2266280X-RAY DIFFRACTION98.4774
1.847-1.9120.283370.236040X-RAY DIFFRACTION98.7763
1.912-1.9840.2723350.2245867X-RAY DIFFRACTION99.0102
1.984-2.0650.2623180.2185641X-RAY DIFFRACTION99.1349
2.065-2.1570.2722580.2175442X-RAY DIFFRACTION99.2513
2.157-2.2620.2542700.2245196X-RAY DIFFRACTION99.2735
2.262-2.3850.2582720.2114960X-RAY DIFFRACTION99.1285
2.385-2.5290.2642530.2164648X-RAY DIFFRACTION99.6341
2.529-2.7040.2512300.2134397X-RAY DIFFRACTION99.4199
2.704-2.920.2581990.2254136X-RAY DIFFRACTION99.7699
2.92-3.1990.2411720.2163829X-RAY DIFFRACTION99.7258
3.199-3.5760.2521850.2283403X-RAY DIFFRACTION99.8608
3.576-4.1280.2211550.2163006X-RAY DIFFRACTION99.9368
4.128-5.0530.2511320.2122564X-RAY DIFFRACTION99.9629
5.053-7.1350.271850.2351992X-RAY DIFFRACTION100

+
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