[English] 日本語
Yorodumi
- PDB-1e6d: PHOTOSYNTHETIC REACTION CENTER MUTANT WITH TRP M115 REPLACED WITH... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1e6d
TitlePHOTOSYNTHETIC REACTION CENTER MUTANT WITH TRP M115 REPLACED WITH PHE (CHAIN M, WM115F) PHE M197 REPLACED WITH ARG (CHAIN M, FM197R)
Components(PHOTOSYNTHETIC REACTION CENTER ...) x 3
KeywordsPHOTOSYNTHESIS / TRANSMEMBRANE / ELECTRON TRANSPORT
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 / membrane => GO:0016020 / metal ion binding
Similarity search - Function
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 / 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 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 / 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 / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / PHOSPHATE ION / SPEROIDENONE / UBIQUINONE-10 / Reaction center protein M chain / Reaction center protein L chain / Reaction center protein H chain / Reaction center protein L chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / PHOSPHATE ION / SPEROIDENONE / UBIQUINONE-10 / Reaction center protein M chain / Reaction center protein L chain / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Reaction center protein H chain
Similarity search - Component
Biological speciesRHODOBACTER SPHAEROIDES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRidge, J.P. / Fyfe, P.K. / McAuley, K.E. / Van Brederode, M.E. / Robert, B. / Van Grondelle, R. / Isaacs, N.W. / Cogdell, R.J. / Jones, M.R.
Citation
Journal: Biochem.J. / Year: 2000
Title: An Examination of How Structural Changes Can Affect the Rate of Electron Transfer in a Mutated Bacterial Photoreaction Centre
Authors: Ridge, J.P. / Fyfe, P.K. / Mcauley, K.E. / Van Brederode, M.E. / Robert, B. / Van Grondelle, R. / Isaacs, N.W. / Cogdell, R.J. / Jones, M.R.
#1: Journal: Biochemistry / Year: 2000
Title: Structural Consequences of the Replacement of Glycine M203 with Aspartic Acid in the Reaction Center from Rhodobacter Sphaeroides
Authors: Fyfe, P.K. / Ridge, J.P. / Mcauley, K.E. / Cogdell, R.J. / Isaacs, N.W. / Jones, M.R.
#2: Journal: Biochemistry / Year: 1998
Title: Structural Studies of Wild-Type and Mutant Reaction Centers from an Antenna-Deficient Strain of Rhodobacter Sphaeroides: Monitoring the Optical Properties of the Complex from Bacterial Cell to Crystal
Authors: Mcauley, K.E. / Fyfe, P.K. / Ridge, J.P. / Prince, S.M. / Hunter, C.N. / Isaacs, N.W. / Cogdell, R.J. / Jones, M.R.
#3: Journal: Photosyn. Res. / Year: 1998
Title: Crystallographic Studies of Mutant Reaction Centers from Rhodobacter Sphaeroides
Authors: Fyfe, P.K. / Mcauley-Hecht, K.E. / Ridge, J.P. / Prince, S.M. / Fritzsch, G. / Isaacs, N.W. / Cogdell, R.J. / Jones, M.R.
History
DepositionAug 11, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_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_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 / _struct_conn.pdbx_dist_value / _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
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
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)103,38022
Polymers93,7823
Non-polymers9,59819
Water3,819212
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37730 Å2
ΔGint-235.9 kcal/mol
Surface area28720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.200, 141.200, 187.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

-
PHOTOSYNTHETIC REACTION CENTER ... , 3 types, 3 molecules HLM

#1: Protein PHOTOSYNTHETIC REACTION CENTER H SUBUNIT


Mass: 28066.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Cellular location: CYTOPLASMIC MEMBRANE / Gene: PUFQLMX / Plasmid: PRKEH10D / Gene (production host): PUFQLMX / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): WM115F/FM197R / References: UniProt: P11846, UniProt: P0C0Y7*PLUS
#2: Protein PHOTOSYNTHETIC REACTION CENTER L SUBUNIT


Mass: 31346.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Cellular location: CYTOPLASMIC MEMBRANE / Gene: PUFQLMX / Plasmid: PRKEH10D / Gene (production host): PUFQLMX / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): WM115F/FM197R / References: UniProt: P02954, UniProt: P0C0Y8*PLUS
#3: Protein PHOTOSYNTHETIC REACTION CENTER M SUBUNIT


Mass: 34369.523 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Cellular location: CYTOPLASMIC MEMBRANE / Gene: PUFQLMX / Plasmid: PRKEH10D / Gene (production host): PUFQLMX / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): WM115F/FM197R / References: UniProt: P02953, UniProt: P0C0Y9*PLUS

-
Non-polymers , 8 types, 231 molecules

#4: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#6: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#7: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#8: Chemical ChemComp-FE / FE (III) ION


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


Mass: 594.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H70O2
#10: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsCHAIN M ENGINEERED MUTATION TRP115PHE, PHE197ARG THE PHOTOSYNTHETIC REACTION CENTER MEDIATES THE ...CHAIN M ENGINEERED MUTATION TRP115PHE, PHE197ARG THE PHOTOSYNTHETIC REACTION CENTER MEDIATES THE INITIAL PHOTOCHEMICAL EVENT IN THE ELECTRON TRANSFER PROCESS OF PHOTOSYNTHESIS.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 7

-
Sample preparation

CrystalDensity Matthews: 5.4 Å3/Da / Density % sol: 75.2 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19 mg/mlprotein1drop
20.09 %(v/v)lauryldimethylamine oxide1drop
33.5 %(w/v)1.2.3-heptanetriol1drop
40.75 Mpotassium phosphate1drop
51.5 Mpotassium phosphate1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.3→26.4 Å / Num. obs: 90885 / % possible obs: 94.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.11
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.53 / % possible all: 71.2
Reflection
*PLUS
Rmerge(I) obs: 0.11
Reflection shell
*PLUS
% possible obs: 71.2 % / Rmerge(I) obs: 0.53

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD-TYPE RHODOBACTER SPHAEROIDES COORDINATES (UNPUBLISHED DATA)

Resolution: 2.3→26.4 Å / SU B: 4.34 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.14
RfactorNum. reflection% reflectionSelection details
Rfree0.2 -5 %RANDOM
Rwork0.174 ---
obs-90885 94.5 %-
Displacement parametersBiso mean: 38.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→26.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6466 0 656 212 7334
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0260.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.030.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5562
X-RAY DIFFRACTIONp_mcangle_it2.4093
X-RAY DIFFRACTIONp_scbond_it1.7952
X-RAY DIFFRACTIONp_scangle_it2.8933
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.33
X-RAY DIFFRACTIONp_staggered_tor16.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.120
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.174 / Rfactor Rfree: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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