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- PDB-5m7k: Blastochloris viridis photosynthetic reaction center - RC_vir_xfel -

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Basic information

Entry
Database: PDB / ID: 5m7k
TitleBlastochloris viridis photosynthetic reaction center - RC_vir_xfel
Components
  • (Reaction center protein ...Photosynthetic reaction centre) x 3
  • Photosynthetic reaction center cytochrome c subunit
KeywordsPHOTOSYNTHESIS / Photosynthetic / Reaction Center
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 / 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 Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 ...Photosynthetic Reaction Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / 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. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN B / DIACYL GLYCEROL / : / HEME C / Chem-MPG / MENAQUINONE-7 / 15-cis-1,2-dihydroneurosporene / Chem-OTP / PHOSPHATE ION ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN B / DIACYL GLYCEROL / : / HEME C / Chem-MPG / MENAQUINONE-7 / 15-cis-1,2-dihydroneurosporene / Chem-OTP / PHOSPHATE ION / 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: 3.5 Å
AuthorsSharma, A.S. / Johansson, L. / Dunevall, E. / Wahlgren, W.Y. / Neutze, R. / Katona, G.
CitationJournal: Acta Crystallogr A Found Adv / Year: 2017
Title: Asymmetry in serial femtosecond crystallography data.
Authors: Sharma, A. / Johansson, L. / Dunevall, E. / Wahlgren, W.Y. / Neutze, R. / Katona, G.
History
DepositionOct 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Nov 14, 2018Group: Advisory / Data collection
Category: diffrn / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jan 17, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosynthetic reaction center cytochrome c subunit
B: Reaction center protein L chain
C: Reaction center protein M chain
D: Reaction center protein H chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,38824
Polymers134,6404
Non-polymers11,74820
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50170 Å2
ΔGint-370 kcal/mol
Surface area40280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.900, 84.800, 384.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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 BCD

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


Mass: 30600.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06009
#3: Protein Reaction center protein M chain / Photosynthetic reaction centre / Photosynthetic reaction center M subunit


Mass: 36063.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06010
#4: Protein Reaction center protein H chain / Photosynthetic reaction centre / 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

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Non-polymers , 10 types, 20 molecules

#5: Chemical
ChemComp-HEC / HEME C / Heme C


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


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#7: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


Mass: 911.504 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#8: Chemical ChemComp-BPB / BACTERIOPHEOPHYTIN B / Pheophytin


Mass: 887.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O6
#9: Chemical ChemComp-MPG / [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#10: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#11: Chemical ChemComp-MQ7 / MENAQUINONE-7 / Vitamin K2


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


Mass: 540.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H60
#13: Chemical ChemComp-OTP / (2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE / OCTAPRENYL PYROPHOSPHATE


Mass: 722.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H68O7P2
#14: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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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: batch mode
Details: Melted monoolein was thoroughly mixed in a ratio of 3:2 (v/v) with 0.1M HEPES, pH 7.5, 0.1 % LDAO until a viscous, transparent LCP was obtained. The formed phase was then transferred into a ...Details: Melted monoolein was thoroughly mixed in a ratio of 3:2 (v/v) with 0.1M HEPES, pH 7.5, 0.1 % LDAO until a viscous, transparent LCP was obtained. The formed phase was then transferred into a glass vial and sponge-phase-inducing solution (1:4 ratio) was added containing 16% Jeffamine M-600, 1M HEPES pH 7.9, 0.7 M Ammonium sulphate, 2.5% 1,2,3-Heptanetriol, which swell the cubic phase to sponge phase. After phase separation overnight, the upper phase (sponge phase) was harvested. Crystals were grown using batch crystallization in the lipidic-sponge phase. Equal amount of sponge phase and protein were mixed with 2/5 (v/v) of 1.2 M Tris-sodium citrate and allowed to incubate for several weeks.

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.32 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Feb 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.32 Å / Relative weight: 1
ReflectionResolution: 3.5→58 Å / Num. obs: 25004 / % possible obs: 99.4 % / Redundancy: 59 % / Net I/σ(I): 3.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
CrystFEL0.6.2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CAS

4cas


Resolution: 3.5→55.438 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3
RfactorNum. reflection% reflection
Rfree0.2738 1294 5.19 %
Rwork0.2529 --
obs0.254 24926 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.5→55.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9076 0 805 0 9881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310255
X-RAY DIFFRACTIONf_angle_d0.71214102
X-RAY DIFFRACTIONf_dihedral_angle_d11.8465631
X-RAY DIFFRACTIONf_chiral_restr0.041430
X-RAY DIFFRACTIONf_plane_restr0.0041773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.64010.31841440.28562565X-RAY DIFFRACTION100
3.6401-3.80570.32761420.28462586X-RAY DIFFRACTION100
3.8057-4.00630.2991520.27932544X-RAY DIFFRACTION100
4.0063-4.25730.31221410.27062588X-RAY DIFFRACTION100
4.2573-4.58580.27521120.252619X-RAY DIFFRACTION100
4.5858-5.0470.26281390.232614X-RAY DIFFRACTION100
5.047-5.77670.25391510.23572647X-RAY DIFFRACTION100
5.7767-7.27540.25441550.23862654X-RAY DIFFRACTION100
7.2754-55.44480.2391580.24542815X-RAY DIFFRACTION100

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