[English] 日本語
Yorodumi
- PDB-9s39: Serial crystallography structure of a photosynthetic reaction cen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9s39
TitleSerial crystallography structure of a photosynthetic reaction center using a goniometer-compatible 96-well chip-based platform
Components
  • (Reaction center protein ...) x 3
  • FME-TYR-HIS-GLY-ALA-LEU-ALA-GLN
  • Photosynthetic reaction center cytochrome c subunit
KeywordsPHOTOSYNTHESIS / Reaction center blastochloris viridis structure
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / 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, H subunit, N-terminal / PRC-barrel domain / 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, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / Photosynthetic reaction centre, M subunit / PRC-barrel domain / PRC-barrel-like superfamily / Photosynthetic reaction centre, L subunit / 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 / : / HEME C / MENAQUINONE-7 / 15-cis-1,2-dihydroneurosporene / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGhosh, S. / Banacore, A.
Funding support Sweden, European Union, 7items
OrganizationGrant numberCountry
Swedish Research Council201706734 Sweden
Swedish Research Council202105662 Sweden
Swedish Research Council202105981 Sweden
The Swedish Foundation for Strategic ResearchID170060 Sweden
European Research Council (ERC)789030European Union
European Research Council (ERC)963936European Union
Swedish Research Council201500560 Sweden
CitationJournal: J.Appl.Crystallogr. / Year: 2026
Title: A user-friendly goniometer-compatible fixed-target platform for macromolecular crystallography at synchrotrons.
Authors: Ghosh, S. / Banacore, A. / Norder, P. / Bjelcic, M. / Kabbinale, A. / Nileshwar, P. / Wehlander, G. / de Sanctis, D. / Basu, S. / Orlans, J. / Vallejos, A. / Chavas, L.M.G. / Neutze, R. / Branden, G.
History
DepositionJul 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Photosynthetic reaction center cytochrome c subunit
H: Reaction center protein H chain
L: Reaction center protein L chain
M: Reaction center protein M chain
D: FME-TYR-HIS-GLY-ALA-LEU-ALA-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,19326
Polymers131,2925
Non-polymers9,90121
Water88349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area47920 Å2
ΔGint-485 kcal/mol
Surface area40610 Å2
Unit cell
Length a, b, c (Å)226.5, 226.5, 113.9
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

-
Components

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

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


Mass: 26863.398 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

-
Protein / Protein/peptide , 2 types, 2 molecules CD

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


Mass: 37108.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P07173
#5: Protein/peptide FME-TYR-HIS-GLY-ALA-LEU-ALA-GLN


Mass: 919.036 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Extra added fragment of H subunit / Source: (natural) Blastochloris viridis (bacteria)

-
Non-polymers , 8 types, 70 molecules

#6: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-BCB / BACTERIOCHLOROPHYLL B


Mass: 909.488 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H72MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-BPB / BACTERIOPHEOPHYTIN B


Mass: 887.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O6 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-MQ7 / MENAQUINONE-7


Mass: 648.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H64O2 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-NS5 / 15-cis-1,2-dihydroneurosporene


Mass: 540.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H60 / Feature type: SUBJECT OF INVESTIGATION
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.56 Å3/Da / Density % sol: 77.89 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: heptane-triol, KPi, Ammonium Sulphate

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Apr 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 3.3→113 Å / Num. obs: 72801 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.99 / Net I/σ(I): 6.6
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 6.6 % / Num. unique obs: 8265 / CC1/2: 0.43 / CC star: 0.658 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
CrystFELdata reduction
CrystFELdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→60 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.903 / SU B: 29.994 / SU ML: 0.458 / Cross valid method: FREE R-VALUE / ESU R: 0.599 / ESU R Free: 0.384
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2963 2997 5.074 %
Rwork0.2462 56066 -
all0.249 --
obs-59063 98.946 %
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: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.632 Å2-0 Å2-0 Å2
2--1.632 Å2-0 Å2
3----3.264 Å2
Refinement stepCycle: LAST / Resolution: 3.3→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9291 0 695 49 10035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01210350
X-RAY DIFFRACTIONr_bond_other_d0.0030.0169351
X-RAY DIFFRACTIONr_angle_refined_deg2.2851.85614245
X-RAY DIFFRACTIONr_angle_other_deg0.8521.72621454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.59751199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.165214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.944101401
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.87810419
X-RAY DIFFRACTIONr_chiral_restr0.1680.21446
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212483
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022471
X-RAY DIFFRACTIONr_nbd_refined0.2320.22357
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.28960
X-RAY DIFFRACTIONr_nbtor_refined0.180.24962
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.25094
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2186
X-RAY DIFFRACTIONr_metal_ion_refined0.0770.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2980.219
X-RAY DIFFRACTIONr_nbd_other0.2040.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.26
X-RAY DIFFRACTIONr_mcbond_it11.6889.7534706
X-RAY DIFFRACTIONr_mcbond_other11.6869.7544706
X-RAY DIFFRACTIONr_mcangle_it16.87617.5385869
X-RAY DIFFRACTIONr_mcangle_other16.87917.5395870
X-RAY DIFFRACTIONr_scbond_it11.88410.0335644
X-RAY DIFFRACTIONr_scbond_other11.88310.0355645
X-RAY DIFFRACTIONr_scangle_it17.56618.2938376
X-RAY DIFFRACTIONr_scangle_other17.56518.2948377
X-RAY DIFFRACTIONr_lrange_it21.403115.93341706
X-RAY DIFFRACTIONr_lrange_other21.403115.93441707
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.50.4762000.4394081X-RAY DIFFRACTION99.0743
3.5-3.70.4552230.4263972X-RAY DIFFRACTION98.8454
3.7-3.90.4162240.4163846X-RAY DIFFRACTION98.6189
3.9-4.10.4492250.3963711X-RAY DIFFRACTION98.2772
4.1-4.30.4061600.373671X-RAY DIFFRACTION98.534
4.241-4.470.2811610.1952894X-RAY DIFFRACTION99.3496
4.3-4.50.4151740.3773501X-RAY DIFFRACTION97.5577
4.47-4.7410.2451640.1842749X-RAY DIFFRACTION99.4877
4.5-4.70.4081800.323388X-RAY DIFFRACTION98.1298
4.7-4.90.3131810.2583319X-RAY DIFFRACTION99.2908
4.741-5.0680.2581350.22598X-RAY DIFFRACTION99.4903
4.9-5.10.291740.2363169X-RAY DIFFRACTION99.2872
5.068-5.4730.3011240.2082432X-RAY DIFFRACTION99.3007
5.1-5.30.2551650.1983047X-RAY DIFFRACTION99.6278
5.473-5.9940.2491100.1852261X-RAY DIFFRACTION99.4964
5.994-6.6990.2481070.1762047X-RAY DIFFRACTION99.1713
6.699-7.7310.222760.161841X-RAY DIFFRACTION99.8438
7.731-9.4570.176910.1411564X-RAY DIFFRACTION99.5788
9.457-13.3280.201750.1661228X-RAY DIFFRACTION99.5416
13.328-600.344460.387723X-RAY DIFFRACTION97.2187

+
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