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- PDB-9vdx: Serial synchrotron crystallography structure of a photosynthetic ... -

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Basic information

Entry
Database: PDB / ID: 9vdx
TitleSerial synchrotron crystallography structure of a photosynthetic reaction center using a goniometer-compatible chip-based platform
Components
  • (Reaction center protein ...) x 3
  • Photosynthetic reaction center cytochrome c subunit
KeywordsMEMBRANE PROTEIN / Bioenergetics / photosynthesis / serial crystallography
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 / DIACYL GLYCEROL / : / HEME C / HEPTANE-1,2,3-TRIOL / MENAQUINONE-7 / 15-cis-1,2-dihydroneurosporene / Reaction center protein H chain / Reaction center protein L chain ...BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / DIACYL GLYCEROL / : / HEME C / HEPTANE-1,2,3-TRIOL / 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: 2.8 Å
AuthorsGhosh, S. / Banacore, A. / Neutze, R. / Branden, G.
Funding supportEuropean Union, Sweden, 4items
OrganizationGrant numberCountry
European Research Council (ERC)789030 and 963936European Union
Swedish Research Council2017-06734, 2021-05662 and 2021-05981 Sweden
Swedish Research Council2015-00560 Sweden
The Swedish Foundation for Strategic ResearchID17-0060 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. / Vallejos, L.M.G. / Neutze, R. / Branden, G.
History
DepositionJun 9, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,65843
Polymers132,4104
Non-polymers13,24839
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53690 Å2
ΔGint-547 kcal/mol
Surface area41390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.800, 223.800, 113.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules C

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


Mass: 37450.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P07173

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

#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

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Non-polymers , 11 types, 135 molecules

#5: Chemical
ChemComp-HEC / HEME C


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


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H31NO / Feature type: SUBJECT OF INVESTIGATION / Comment: LDAO, detergent*YM
#9: Chemical ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H16O3 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-BCB / BACTERIOCHLOROPHYLL B


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


Mass: 887.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O6 / Feature type: SUBJECT OF INVESTIGATION
#12: 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
#13: Chemical ChemComp-MQ7 / MENAQUINONE-7


Mass: 648.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H64O2 / Feature type: SUBJECT OF INVESTIGATION
#14: 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
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 5.37 Å3/Da / Density % sol: 77.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 400 microliter heptane-triol, 20 microliter 1M Potassium Phosphate pH 6.8, 475mg Ammonium Sulphate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→37 Å / Num. obs: 151216 / % possible obs: 100 % / Redundancy: 412 % / CC1/2: 0.936 / Net I/σ(I): 4.1
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 6866 / CC1/2: 0.529
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
MxCuBE5.8.0405data collection
CrystFELdata reduction
PHASERphasing
REFMAC8.0.010refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→36.8 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.891 / SU B: 13.534 / SU ML: 0.257 / Cross valid method: FREE R-VALUE / ESU R: 0.374 / ESU R Free: 0.279
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.253 3534 4.98 %
Rwork0.215 67431 -
all0.21 --
obs-70965 99.629 %
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: 50.965 Å2
Baniso -1Baniso -2Baniso -3
1-0.505 Å20 Å20 Å2
2--0.505 Å20 Å2
3----1.011 Å2
Refinement stepCycle: LAST / Resolution: 2.8→36.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9346 0 909 96 10351
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01210619
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169932
X-RAY DIFFRACTIONr_angle_refined_deg2.1911.75114548
X-RAY DIFFRACTIONr_angle_other_deg0.5831.66922734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.30251182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.699565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.989101413
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.11310419
X-RAY DIFFRACTIONr_chiral_restr0.0710.21480
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212028
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022512
X-RAY DIFFRACTIONr_nbd_refined0.2490.22424
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.29668
X-RAY DIFFRACTIONr_nbtor_refined0.1930.25072
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.25462
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2310
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0610.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2460.211
X-RAY DIFFRACTIONr_nbd_other0.1180.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0480.24
X-RAY DIFFRACTIONr_mcbond_it4.334.8564740
X-RAY DIFFRACTIONr_mcbond_other4.3294.8564740
X-RAY DIFFRACTIONr_mcangle_it6.6358.735918
X-RAY DIFFRACTIONr_mcangle_other6.6348.735919
X-RAY DIFFRACTIONr_scbond_it4.6775.2945879
X-RAY DIFFRACTIONr_scbond_other4.6775.2945880
X-RAY DIFFRACTIONr_scangle_it7.3089.5398630
X-RAY DIFFRACTIONr_scangle_other7.3089.5398631
X-RAY DIFFRACTIONr_lrange_it11.42146.62312553
X-RAY DIFFRACTIONr_lrange_other11.42446.6312550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.8720.3262270.284819X-RAY DIFFRACTION97.696
2.872-2.9510.2992470.274720X-RAY DIFFRACTION98.337
2.951-3.0350.3142400.2824643X-RAY DIFFRACTION99.8569
3.035-3.1280.2782080.2594556X-RAY DIFFRACTION100
3.128-3.230.3232430.2534383X-RAY DIFFRACTION100
3.23-3.3430.282420.2334239X-RAY DIFFRACTION100
3.343-3.4680.2782590.2334051X-RAY DIFFRACTION100
3.468-3.6080.2712040.2113986X-RAY DIFFRACTION100
3.608-3.7670.291810.2383805X-RAY DIFFRACTION99.7997
3.767-3.9480.2512040.23645X-RAY DIFFRACTION100
3.948-4.1590.241690.1893499X-RAY DIFFRACTION100
4.159-4.4080.2091610.1683319X-RAY DIFFRACTION100
4.408-4.7080.211780.1683093X-RAY DIFFRACTION100
4.708-5.0780.2231650.1692903X-RAY DIFFRACTION100
5.078-5.5520.2231380.1772704X-RAY DIFFRACTION100
5.552-6.190.1961210.182475X-RAY DIFFRACTION100
6.19-7.1150.2371200.1782193X-RAY DIFFRACTION100
7.115-8.6350.2271130.1791884X-RAY DIFFRACTION100
8.635-11.8920.163640.1691520X-RAY DIFFRACTION100
11.892-36.80.27490.282975X-RAY DIFFRACTION100

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