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- PDB-3t6e: Crystal Structure of the Reaction Centre from Blastochloris virid... -

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Basic information

Entry
Database: PDB / ID: 3t6e
TitleCrystal Structure of the Reaction Centre from Blastochloris viridis strain DSM 133 (ATCC 19567) substrain-94
Components
  • (Reaction center protein ...) x 3
  • Photosynthetic reaction center cytochrome c subunit
KeywordsELECTRON TRANSPORT / Pigment-protein complex / Electron transfer / Photosynthesis / Photosynthetic reaction center / Photosynthetic membranes / Evolution / Genetic drift
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 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; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center, subunit M; 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; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / 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 / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / 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. / Few Secondary Structures / Irregular / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / DIACYL GLYCEROL / : / HEME C / HEPTANE-1,2,3-TRIOL / MENAQUINONE-9 / 15-cis-1,2-dihydroneurosporene / Ubiquinone-9 / Reaction center protein H chain ...BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / DIACYL GLYCEROL / : / HEME C / HEPTANE-1,2,3-TRIOL / MENAQUINONE-9 / 15-cis-1,2-dihydroneurosporene / Ubiquinone-9 / 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: 1.92 Å
AuthorsRoszak, A.W. / Gardiner, A.T. / Isaacs, N.W. / Cogdell, R.J.
CitationJournal: Biochem.J. / Year: 2012
Title: New insights into the structure of the reaction centre from Blastochloris viridis: evolution in the laboratory.
Authors: Roszak, A.W. / Moulisova, V. / Reksodipuro, A.D. / Gardiner, A.T. / Fujii, R. / Hashimoto, H. / Isaacs, N.W. / Cogdell, R.J.
History
DepositionJul 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_validate_chiral
Item: _chem_comp_atom.atom_id / _chem_comp_atom.pdbx_aromatic_flag ..._chem_comp_atom.atom_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_bond.atom_id_2 / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.pdbx_stereo_config
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)158,882114
Polymers134,3944
Non-polymers24,488110
Water17,547974
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area62160 Å2
ΔGint-650 kcal/mol
Surface area41970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.583, 221.583, 113.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11H-864-

HOH

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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: 39419.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: substrain-94 is identical at the amino acid level with the original strain DSM 133
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
Details: substrain-94 is identical at the amino acid level with the original strain DSM 133
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
Details: substrain-94 is identical at the amino acid level with the original strain DSM 133
Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06009
#4: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 35948.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: substrain-94 is identical at the amino acid level with the original strain DSM 133
Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: P06010

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Non-polymers , 13 types, 1084 molecules

#5: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#7: Chemical
ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C39H76O5
#8: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: SO4
#9: Chemical
ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H16O3
#10: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical
ChemComp-BCB / BACTERIOCHLOROPHYLL B


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


Mass: 887.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O6
#13: Chemical ChemComp-UQ9 / Ubiquinone-9 / 2,3-dimethoxy-5-methyl-6-[(2E,6E,10E,14Z,18E,22E,26E,30Z)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,6,10,14,18 ,22,26,30,34-nonaen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 795.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C54H82O4
#14: Chemical ChemComp-MQ9 / MENAQUINONE-9


Mass: 785.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C56H80O2
#15: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#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.: 974 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein in 20 mM sodium phosphate buffer and 0.1% lauryldimethylamine N,N-oxide (LDAO) detergent, precipitant 1.5 M ammonium sulfate, amphiphile 3% heptanetriol, reservoir solution 2.2-2.4 M ...Details: Protein in 20 mM sodium phosphate buffer and 0.1% lauryldimethylamine N,N-oxide (LDAO) detergent, precipitant 1.5 M ammonium sulfate, amphiphile 3% heptanetriol, reservoir solution 2.2-2.4 M ammonium sulphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9194 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2010 / Details: Mirrors
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9194 Å / Relative weight: 1
ReflectionResolution: 1.92→43.46 Å / Num. all: 212134 / Num. obs: 212134 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.35 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.119 / Net I/σ(I): 9.4
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 18.87 % / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 1.6 / Num. unique all: 20895 / Rsym value: 0.843 / % possible all: 99.1

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.6.0101refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3T6D

3t6d


Resolution: 1.92→43.46 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.678 / SU ML: 0.059 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17804 10638 5 %RANDOM
Rwork0.15483 ---
all0.15598 211844 --
obs0.15598 201206 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å2-0 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.92→43.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9340 0 1586 974 11900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02211418
X-RAY DIFFRACTIONr_bond_other_d0.0020.027894
X-RAY DIFFRACTIONr_angle_refined_deg2.232.08515549
X-RAY DIFFRACTIONr_angle_other_deg1.0213.00518646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8325.0161219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71522.389427
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.142151432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8731567
X-RAY DIFFRACTIONr_chiral_restr0.110.21577
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111935
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022291
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 761 -
Rwork0.266 14042 -
obs-14803 99.27 %
Refinement TLS params.Method: refined / Origin x: -0.595 Å / Origin y: -49.212 Å / Origin z: 10.558 Å
111213212223313233
T0.036 Å20.0089 Å2-0.0216 Å2-0.082 Å2-0.0368 Å2--0.0291 Å2
L0.5286 °20.3367 °2-0.0204 °2-0.6443 °2-0.0853 °2--0.3241 °2
S-0.0226 Å °0.1253 Å °-0.0536 Å °-0.0487 Å °0.0521 Å °-0.0119 Å °-0.0131 Å °0.0394 Å °-0.0295 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 334
2X-RAY DIFFRACTION1H1 - 45
3X-RAY DIFFRACTION1H54 - 258
4X-RAY DIFFRACTION1M501
5X-RAY DIFFRACTION1L1 - 273
6X-RAY DIFFRACTION1L503
7X-RAY DIFFRACTION1H701 - 733
8X-RAY DIFFRACTION1C712 - 730
9X-RAY DIFFRACTION1M702 - 732
10X-RAY DIFFRACTION1L703 - 731
11X-RAY DIFFRACTION1H259 - 265
12X-RAY DIFFRACTION1H266 - 268
13X-RAY DIFFRACTION1H269 - 279

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