[English] 日本語
Yorodumi
- PDB-5vjt: De Novo Photosynthetic Reaction Center Protein Equipped with Heme... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vjt
TitleDe Novo Photosynthetic Reaction Center Protein Equipped with Heme B and Zn(II) cations
ComponentsReaction Center Maquette
KeywordsDE NOVO PROTEIN / maquette / protein design / charge separation / artificial photosynthesis
Function / homologyPROTOPORPHYRIN IX CONTAINING FE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsEnnist, N.M. / Stayrook, S.E. / Dutton, P.L. / Moser, C.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DESC0001035 United States
CitationJournal: Nat Commun / Year: 2022
Title: De novo protein design of photochemical reaction centers.
Authors: Ennist, N.M. / Zhao, Z. / Stayrook, S.E. / Discher, B.M. / Dutton, P.L. / Moser, C.C.
History
DepositionApr 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Reaction Center Maquette
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3847
Polymers22,5301
Non-polymers8546
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.747, 43.747, 245.522
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-348-

HOH

21A-362-

HOH

-
Components

#1: Protein Reaction Center Maquette


Mass: 22530.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: de novo designed protein / Source: (gene. exp.) synthetic construct (others) / Gene: designed / Plasmid: pJ414 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.82 % / Description: octahedron
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 2.7 M NaCl, 100 mM Na acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 20, 2013 / Details: Oxford Danfysik toroidal focusing mirror
RadiationMonochromator: channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.45→41.21 Å / Num. obs: 43568 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.779 % / Biso Wilson estimate: 23.325 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.105 / Χ2: 0.953 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.45-1.495.2251.3371.2630250.6841.48496.1
1.49-1.537.9941.1252.1730830.9231.20299.8
1.53-1.588.9651.3541.9230050.7761.436100
1.58-1.629.0231.1322.3529290.8011.199100
1.62-1.689.1610.932.8728240.8570.984100
1.68-1.749.2210.8143.2327110.9020.862100
1.74-1.89.3080.5924.3926510.940.626100
1.8-1.879.3360.4755.4425790.9570.503100
1.87-1.969.3330.3587.0824610.9820.379100
1.96-2.059.2720.23610.3823510.9850.249100
2.05-2.169.3760.15814.9522620.9920.167100
2.16-2.39.3360.12318.5921620.9950.13100
2.3-2.459.2850.09522.9320100.9970.101100
2.45-2.659.30.07130.1718820.9980.075100
2.65-2.99.1760.06133.4217670.9990.065100
2.9-3.259.1320.04542.8315960.9990.04899.9
3.25-3.758.8890.03256.5514300.9990.03499.9
3.75-4.598.6230.02763.96123810.02899.9
4.59-6.498.3620.02858.8999710.0399.6
6.49-41.216.9290.02659.8160510.02898.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEVERSION July 4, 2012 BUILT=20130706data scaling
PHASERphasing
REFMAC5.8.0131refinement
PDB_EXTRACT3.22data extraction
XDSVERSION March 30, 2013data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→41.21 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.103 / SU ML: 0.072 / SU R Cruickshank DPI: 0.0699 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.074
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 2193 5 %RANDOM
Rwork0.2018 ---
obs0.2034 41378 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 71.57 Å2 / Biso mean: 23.274 Å2 / Biso min: 11.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.45→41.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1585 0 91 172 1848
Biso mean--18.34 34.95 -
Num. residues----196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0191729
X-RAY DIFFRACTIONr_bond_other_d0.0030.021699
X-RAY DIFFRACTIONr_angle_refined_deg2.2362.0652334
X-RAY DIFFRACTIONr_angle_other_deg1.0733909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2885201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.21527.47391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34615354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.636157
X-RAY DIFFRACTIONr_chiral_restr0.1560.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022009
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02390
LS refinement shellResolution: 1.452→1.489 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 156 -
Rwork0.373 2848 -
all-3004 -
obs--95.52 %

+
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