[English] 日本語
Yorodumi
- PDB-7q7q: LIPIDIC CUBIC PHASE SERIAL FEMTOSECOND CRYSTALLOGRAPHY STRUCTURE ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q7q
TitleLIPIDIC CUBIC PHASE SERIAL FEMTOSECOND CRYSTALLOGRAPHY STRUCTURE OF A PHOTOSYNTHETIC REACTION CENTRE
Components
  • (Reaction center protein ...) x 3
  • Photosynthetic reaction center cytochrome c subunit
KeywordsMEMBRANE PROTEIN / CRYSTALLOGRAPHY STRUCTURE PHOTOSYNTHETIC REACTION CENTRE
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / photosynthetic electron transport in photosystem II / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Multiheme cytochrome c family profile. / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Multiheme cytochrome c family profile. / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / DIACYL GLYCEROL / : / HEME C / HEPTANE-1,2,3-TRIOL / MENAQUINONE-9 / 15-cis-1,2-dihydroneurosporene / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / UBIQUINONE-2 ...BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / DIACYL GLYCEROL / : / HEME C / HEPTANE-1,2,3-TRIOL / MENAQUINONE-9 / 15-cis-1,2-dihydroneurosporene / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / UBIQUINONE-2 / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center cytochrome c subunit
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBaath, P. / Banacore, A. / Neutze, R.
Funding supportEuropean Union, Sweden, 2items
OrganizationGrant numberCountry
National Research Development and Innovation Office (NKFIH)789030European Union
European Research Council (ERC)2015-00560 Sweden
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre.
Authors: Bath, P. / Banacore, A. / Borjesson, P. / Bosman, R. / Wickstrand, C. / Safari, C. / Dods, R. / Ghosh, S. / Dahl, P. / Ortolani, G. / Bjorg Ulfarsdottir, T. / Hammarin, G. / Garcia Bonete, M. ...Authors: Bath, P. / Banacore, A. / Borjesson, P. / Bosman, R. / Wickstrand, C. / Safari, C. / Dods, R. / Ghosh, S. / Dahl, P. / Ortolani, G. / Bjorg Ulfarsdottir, T. / Hammarin, G. / Garcia Bonete, M.J. / Vallejos, A. / Ostojic, L. / Edlund, P. / Linse, J.B. / Andersson, R. / Nango, E. / Owada, S. / Tanaka, R. / Tono, K. / Joti, Y. / Nureki, O. / Luo, F. / James, D. / Nass, K. / Johnson, P.J.M. / Knopp, G. / Ozerov, D. / Cirelli, C. / Milne, C. / Iwata, S. / Branden, G. / Neutze, R.
History
DepositionNov 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_validate_chiral
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
CCC: Photosynthetic reaction center cytochrome c subunit
HHH: Reaction center protein H chain
LLL: Reaction center protein L chain
MMM: Reaction center protein M chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,92542
Polymers132,4104
Non-polymers14,51538
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Purity confirmed with spectrophotometer at A830 nm.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56320 Å2
ΔGint-417 kcal/mol
Surface area41090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.660, 125.130, 182.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11MMM-564-

HOH

-
Components

-
Protein , 1 types, 1 molecules CCC

#1: Protein Photosynthetic reaction center cytochrome c subunit / Cytochrome c558/c559


Mass: 37450.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blastochloris viridis (bacteria) / Gene: pufC, cytC, BVIRIDIS_00500 / Production host: Blastochloris viridis (bacteria) / References: UniProt: P07173

-
Reaction center protein ... , 3 types, 3 molecules HHHLLLMMM

#2: Protein Reaction center protein H chain / Photosynthetic reaction center H subunit


Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06008
#3: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 30469.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06009
#4: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 35932.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06010

-
Non-polymers , 13 types, 305 molecules

#5: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#7: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#9: Chemical
ChemComp-BCB / BACTERIOCHLOROPHYLL B


Mass: 909.488 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H72MgN4O6
#10: Chemical ChemComp-BPB / BACTERIOPHEOPHYTIN B


Mass: 887.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O6
#11: Chemical
ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H16O3
#12: Chemical ChemComp-UQ2 / UBIQUINONE-2


Mass: 318.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H26O4
#13: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#14: Chemical ChemComp-MQ9 / MENAQUINONE-9


Mass: 785.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C56H80O2
#15: Chemical ChemComp-NS5 / 15-cis-1,2-dihydroneurosporene


Mass: 540.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H60
#16: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.28 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: This LCP crystallization was performed in wells with 200uL precipitant and 20uL LCP+protein.

-
Data collection

DiffractionMean temperature: 293 K / Ambient temp details: Room Temperature / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESA / Wavelength: 1.102 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Nov 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.102 Å / Relative weight: 1
ReflectionResolution: 2.25→23.702 Å / Num. obs: 92545 / % possible obs: 100 % / Redundancy: 11.888 % / CC1/2: 0.995 / Net I/σ(I): 9.6
Reflection shellResolution: 2.25→2.27 Å / Num. unique obs: 92545 / CC1/2: 0.54
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionFlow rate: 0.047 µL/min / Injector diameter: 75 µm / Injector temperature: 293 K
Serial crystallography data reductionCrystal hits: 260392 / Frames indexed: 160275

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrystFEL0.9.0data reduction
CrystFEL0.9.0data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NJ4

5nj4


Resolution: 2.25→23.702 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.515 / SU ML: 0.126 / Cross valid method: FREE R-VALUE / ESU R: 0.185 / ESU R Free: 0.161
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2028 4602 4.974 %
Rwork0.1678 87913 -
all0.169 --
obs-92515 99.856 %
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: 48.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.613 Å20 Å20 Å2
2--1.99 Å2-0 Å2
3----2.602 Å2
Refinement stepCycle: LAST / Resolution: 2.25→23.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9263 0 1022 267 10552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01310703
X-RAY DIFFRACTIONr_bond_other_d0.0020.01710106
X-RAY DIFFRACTIONr_angle_refined_deg2.131.76214640
X-RAY DIFFRACTIONr_angle_other_deg1.2031.69323128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58151177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.06220.4500
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84151407
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg16.304151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7531566
X-RAY DIFFRACTIONr_chiral_restr0.0740.21267
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211746
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022538
X-RAY DIFFRACTIONr_nbd_refined0.1950.21948
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.29096
X-RAY DIFFRACTIONr_nbtor_refined0.1680.24911
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.24652
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2344
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0860.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0980.26
X-RAY DIFFRACTIONr_nbd_other0.1570.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0620.22
X-RAY DIFFRACTIONr_mcbond_it2.8734.7394705
X-RAY DIFFRACTIONr_mcbond_other2.8714.7384704
X-RAY DIFFRACTIONr_mcangle_it4.3727.1055877
X-RAY DIFFRACTIONr_mcangle_other4.3727.1055878
X-RAY DIFFRACTIONr_scbond_it3.5155.3285998
X-RAY DIFFRACTIONr_scbond_other3.5145.3295999
X-RAY DIFFRACTIONr_scangle_it5.5947.7548761
X-RAY DIFFRACTIONr_scangle_other5.5947.7558762
X-RAY DIFFRACTIONr_lrange_it7.35853.19412043
X-RAY DIFFRACTIONr_lrange_other7.35853.20112044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.3080.3073630.3066412X-RAY DIFFRACTION100
2.308-2.3720.2933140.2836265X-RAY DIFFRACTION100
2.372-2.440.3333410.2726111X-RAY DIFFRACTION100
2.44-2.5160.2772960.2485946X-RAY DIFFRACTION100
2.516-2.5980.2583430.2265697X-RAY DIFFRACTION100
2.598-2.6890.2452840.2075571X-RAY DIFFRACTION100
2.689-2.7910.2242730.1855391X-RAY DIFFRACTION100
2.791-2.9050.1722670.1585199X-RAY DIFFRACTION100
2.905-3.0340.1952510.154983X-RAY DIFFRACTION100
3.034-3.1820.2052360.1554761X-RAY DIFFRACTION100
3.182-3.3540.1722210.1484567X-RAY DIFFRACTION100
3.354-3.5570.182120.1394308X-RAY DIFFRACTION100
3.557-3.8030.1592010.1314080X-RAY DIFFRACTION100
3.803-4.1070.1581960.1283789X-RAY DIFFRACTION100
4.107-4.4990.1481950.1263484X-RAY DIFFRACTION100
4.499-5.030.1651720.133190X-RAY DIFFRACTION100
5.03-5.8070.1821510.1472810X-RAY DIFFRACTION100
5.807-7.110.1941340.1442414X-RAY DIFFRACTION100
7.11-10.0480.138930.1261911X-RAY DIFFRACTION100
10.048-23.7020.705590.504991X-RAY DIFFRACTION88.7574

+
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