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- PDB-3t6d: Crystal Structure of the Reaction Centre from Blastochloris virid... -

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Entry
Database: PDB / ID: 3t6d
TitleCrystal Structure of the Reaction Centre from Blastochloris viridis strain DSM 133 (ATCC 19567) substrain-08
Components(Photosynthetic reaction center ...) x 4
KeywordsELECTRON TRANSPORT / Pigment-protein complex / 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 / endomembrane system / electron transfer activity / iron ion binding ...plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / : / photosynthesis, light reaction / photosynthesis / endomembrane system / electron transfer activity / iron ion binding / heme binding / metal ion binding / membrane
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 / (2S,3R)-heptane-1,2,3-triol / HEPTANE-1,2,3-TRIOL / MENAQUINONE-9 / 15-cis-1,2-dihydroneurosporene / Ubiquinone-9 ...BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / DIACYL GLYCEROL / : / HEME C / (2S,3R)-heptane-1,2,3-triol / HEPTANE-1,2,3-TRIOL / MENAQUINONE-9 / 15-cis-1,2-dihydroneurosporene / Ubiquinone-9 / Photosynthetic reaction center H-subunit / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center cytochrome c subunit / 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: 1.95 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 1.2Oct 21, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / pdbx_struct_conn_angle ...chem_comp / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / reflns_shell / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._chem_comp.pdbx_synonyms / _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_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_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 / _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / 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_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 27, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_chiral
Item: _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config ..._chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.pdbx_stereo_config

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Photosynthetic reaction center cytochrome c subunit
H: Photosynthetic reaction center H-subunit
L: Photosynthetic reaction center L-subunit
M: Photosynthetic reaction center M-subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,382153
Polymers134,4064
Non-polymers27,976149
Water15,511861
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70190 Å2
ΔGint-803 kcal/mol
Surface area42650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.440, 220.440, 113.100
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-291-

GOL

21H-813-

HOH

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Components

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Photosynthetic reaction center ... , 4 types, 4 molecules CHLM

#1: Protein Photosynthetic reaction center cytochrome c subunit


Mass: 39523.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: substrain-08 has evolved in the laboratory from the substrain-94
Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: B8Y5U8, UniProt: P07173*PLUS
#2: Protein Photosynthetic reaction center H-subunit


Mass: 28527.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: substrain-08 has evolved in the laboratory from the substrain-94
Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: B8Y5U3, UniProt: P06008*PLUS
#3: Protein Photosynthetic reaction center L-subunit / Photosynthetic reaction center L subunit


Mass: 30469.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: substrain-08 has evolved in the laboratory from the substrain-94
Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: B8Y5U6, UniProt: P06009*PLUS
#4: Protein Photosynthetic reaction center M-subunit


Mass: 35886.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: substrain-08 has evolved in the laboratory from the substrain-94
Source: (natural) Blastochloris viridis (bacteria) / References: UniProt: B8Y5U7, UniProt: P06010*PLUS

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Non-polymers , 14 types, 1010 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.: 24 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#7: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#8: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 41 / Source method: obtained synthetically / Formula: SO4
#9: Chemical
ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C7H16O3
#10: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 54 / 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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#15: Chemical ChemComp-MQ9 / MENAQUINONE-9


Mass: 785.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C56H80O2
#16: Chemical ChemComp-NS5 / 15-cis-1,2-dihydroneurosporene


Mass: 540.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H60
#17: Chemical ChemComp-HTH / (2S,3R)-heptane-1,2,3-triol / heptane-1,2,3-triol


Mass: 148.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O3
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 861 / 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, 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, 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: ESRF / Beamline: BM14 / Wavelength: 0.97108 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 3, 2007 / Details: Mirrors
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97108 Å / Relative weight: 1
ReflectionResolution: 1.95→48.34 Å / Num. all: 193320 / Num. obs: 193320 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.1
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 19553 / % possible all: 98.6

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Processing

Software
NameVersionClassification
DNAdata collection
AMoREphasing
REFMAC5.6.0101refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Unpublished own 2.3 A model for which the 1DXR model was used in the MR

1dxr


Resolution: 1.95→48.34 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.547 / SU ML: 0.065 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2163 9677 5 %RANDOM
Rwork0.18172 ---
all0.18343 193178 --
obs0.18343 183501 96.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.726 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å2-0 Å2-0 Å2
2--0.69 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9339 0 1836 861 12036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02111525
X-RAY DIFFRACTIONr_bond_other_d0.0010.028032
X-RAY DIFFRACTIONr_angle_refined_deg2.2362.09915659
X-RAY DIFFRACTIONr_angle_other_deg13.00319166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99151196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40322.313428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.413151416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1911568
X-RAY DIFFRACTIONr_chiral_restr0.1070.21607
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02111755
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022284
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 702 -
Rwork0.346 13137 -
obs-13839 98.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6521-0.31380.12740.4611-0.03770.31940.02330.04850.0085-0.096-0.0015-0.06710.01060.0083-0.02190.0503-0.02730.03360.0259-0.01890.0253-61.127-111.1838.965
26.34543.878-6.814632.0757-25.922623.266-1.1591.29460.92472.23370.3398-1.8947-1.0428-0.99460.81921.9601-0.9396-1.11461.10130.2920.7999-54.238-113.15425.646
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C2 - 334
2X-RAY DIFFRACTION1H1 - 45
3X-RAY DIFFRACTION1H54 - 258
4X-RAY DIFFRACTION1M500 - 501
5X-RAY DIFFRACTION1L1 - 273
6X-RAY DIFFRACTION1L503
7X-RAY DIFFRACTION1H701 - 721
8X-RAY DIFFRACTION1C716 - 722
9X-RAY DIFFRACTION1M704 - 717
10X-RAY DIFFRACTION1L702 - 724
11X-RAY DIFFRACTION1H259 - 271
12X-RAY DIFFRACTION1H272 - 274
13X-RAY DIFFRACTION1H275 - 291
14X-RAY DIFFRACTION2C1
15X-RAY DIFFRACTION2C730

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