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- PDB-7q7p: LIPIDIC CUBIC PHASE SERIAL FEMTOSECOND CRYSTALLOGRAPHY STRUCTURE ... -

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Basic information

Entry
Database: PDB / ID: 7q7p
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 PHOTHOSYNTHETIC REACTION CENTRE
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, 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-7 / 15-cis-1,2-dihydroneurosporene / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / UBIQUINONE-1 ...BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / DIACYL GLYCEROL / : / HEME C / HEPTANE-1,2,3-TRIOL / MENAQUINONE-7 / 15-cis-1,2-dihydroneurosporene / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / UBIQUINONE-1 / 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: 2.4 Å
AuthorsBaath, P. / Banacore, A. / Neutze, R.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
National Research Development and Innovation Office (NKFIH)789030European Union
European Research Council (ERC)201500560European Union
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 1.1Oct 12, 2022Group: Derived calculations / Refinement description / Category: atom_type / refine
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _refine.B_iso_mean
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_validate_chiral
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)147,36138
Polymers134,3784
Non-polymers12,98334
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53940 Å2
ΔGint-442 kcal/mol
Surface area41520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.900, 125.300, 182.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules CCC

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


Mass: 39419.176 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 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

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Non-polymers , 13 types, 278 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-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C7H16O3
#8: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#10: Chemical
ChemComp-BCB / BACTERIOCHLOROPHYLL B


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


Mass: 887.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O6
#12: Chemical ChemComp-UQ1 / UBIQUINONE-1


Mass: 250.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18O4
#13: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#14: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#15: Chemical ChemComp-MQ7 / MENAQUINONE-7


Mass: 648.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H64O2
#16: Chemical ChemComp-NS5 / 15-cis-1,2-dihydroneurosporene


Mass: 540.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H60
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.62 Å3/Da / Density % sol: 65.98 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 60:40 monoolein with UQ2, protein 40 mg/mL concentration.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.4 Å
DetectorType: MPCCD / Detector: CCD / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4 Å / Relative weight: 1
ReflectionResolution: 2.4→73.92 Å / Num. obs: 76977 / % possible obs: 100 % / Redundancy: 7.05 % / CC1/2: 0.994 / R split: 0.1057 / Net I/σ(I): 7.87
Reflection shellResolution: 2.4→2.42 Å / Num. unique obs: 76977 / CC1/2: 0.42
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrystFEL0.6.3data reduction
CrystFEL0.6.3data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I5N

2i5n


Resolution: 2.4→73.92 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.447 / SU ML: 0.158 / Cross valid method: FREE R-VALUE / ESU R: 0.231 / ESU R Free: 0.188
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2044 3808 4.951 %
Rwork0.1648 73102 -
all0.167 --
obs-73189 100 %
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: 49 Å2
Baniso -1Baniso -2Baniso -3
1-0.782 Å20 Å2-0 Å2
2--1.757 Å2-0 Å2
3----2.538 Å2
Refinement stepCycle: LAST / Resolution: 2.4→73.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9270 0 912 244 10426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01410541
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179818
X-RAY DIFFRACTIONr_angle_refined_deg2.1521.7614449
X-RAY DIFFRACTIONr_angle_other_deg1.2391.69122454
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8951174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.85920.701485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.288151403
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg6.571151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5261565
X-RAY DIFFRACTIONr_chiral_restr0.080.21267
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211638
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022520
X-RAY DIFFRACTIONr_nbd_refined0.1950.21959
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1770.28927
X-RAY DIFFRACTIONr_nbtor_refined0.170.24910
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.24505
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2315
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0330.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.210
X-RAY DIFFRACTIONr_nbd_other0.1940.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0920.22
X-RAY DIFFRACTIONr_mcbond_it3.1124.6624702
X-RAY DIFFRACTIONr_mcbond_other3.114.6624701
X-RAY DIFFRACTIONr_mcangle_it4.7196.9885871
X-RAY DIFFRACTIONr_mcangle_other4.7196.9885872
X-RAY DIFFRACTIONr_scbond_it3.5895.0885838
X-RAY DIFFRACTIONr_scbond_other3.5895.0885839
X-RAY DIFFRACTIONr_scangle_it5.6797.4478577
X-RAY DIFFRACTIONr_scangle_other5.6787.4488578
X-RAY DIFFRACTIONr_lrange_it7.78251.99211956
X-RAY DIFFRACTIONr_lrange_other7.78251.99711957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.2732580.285210X-RAY DIFFRACTION99.9817
2.53-2.6030.2943000.2655058X-RAY DIFFRACTION99.9813
2.603-2.6830.2932410.2554925X-RAY DIFFRACTION100
2.683-2.7710.272540.2244794X-RAY DIFFRACTION100
2.771-2.8680.2252250.2074624X-RAY DIFFRACTION100
2.868-2.9770.2242380.1814465X-RAY DIFFRACTION100
2.977-3.0980.2182170.174318X-RAY DIFFRACTION100
3.098-3.2360.1981970.1624151X-RAY DIFFRACTION100
3.236-3.3940.192000.1453978X-RAY DIFFRACTION100
3.394-3.5770.1891810.1353802X-RAY DIFFRACTION100
3.577-3.7940.161780.1273572X-RAY DIFFRACTION100
3.794-4.0560.1631770.1263386X-RAY DIFFRACTION100
4.056-4.3810.1571690.1243134X-RAY DIFFRACTION100
4.381-4.7990.171680.1342895X-RAY DIFFRACTION100
4.799-5.3650.1751400.1392649X-RAY DIFFRACTION100
5.365-6.1940.2021230.152341X-RAY DIFFRACTION100
6.194-7.5840.1731060.1282014X-RAY DIFFRACTION100
7.584-10.7160.141800.1151602X-RAY DIFFRACTION100

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