[English] 日本語
Yorodumi
- PDB-3t6d: Crystal Structure of the Reaction Centre from Blastochloris virid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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 / photosynthesis, light reaction / photosynthetic electron transport in photosystem II / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / electron transfer activity / iron ion binding / heme binding ...plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / photosynthetic electron transport in photosystem II / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / electron transfer activity / iron ion binding / heme binding / membrane / 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. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more