[English] 日本語
Yorodumi
- PDB-4bcl: FMO protein from Prosthecochloris aestuarii 2K at Room Temperature -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bcl
TitleFMO protein from Prosthecochloris aestuarii 2K at Room Temperature
ComponentsBACTERIOCHLOROPHYLL A PROTEIN
KeywordsELECTRON TRANSPORT / EXCITATION ENERGY TRANSFER / REACTION CENTER
Function / homology
Function and homology information


bacteriochlorophyll binding / photosynthesis / metal ion binding
Similarity search - Function
Bacteriochlorophyll-a Protein / Bacteriochlorophyll A / Bacteriochlorophyll A protein / Bacteriochlorophyll A superfamily / Bacteriochlorophyll A protein / Clam / Mainly Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / Bacteriochlorophyll a protein
Similarity search - Component
Biological speciesProsthecochloris aestuarii (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsTronrud, D.E. / Matthews, B.W.
Citation
Journal: Photosynthetic Reaction Center / Year: 1993
Title: Refinement of the Structure of a Water-Soluble Antenna Complex from Green Photosynthetic Bacteria by Incorporation of the Chemically Determined Amino Acid Sequence
Authors: Tronrud, D.E. / Matthews, B.W.
#1: Journal: J.Mol.Biol. / Year: 1986
Title: Structure and X-Ray Amino Acid Sequence of a Bacteriochlorophyll a Protein from Prosthecochloris Aestuarii Refined at 1.9 A Resolution
Authors: Tronrud, D.E. / Schmid, M.F. / Matthews, B.W.
#2: Journal: Chem.Scr. / Year: 1983
Title: Structural Studies of a Bacteriochlorophyll-Containing Protein
Authors: Schmid, M.F. / Tronrud, D.E. / Matthews, B.W.
#3: Journal: Lipid-Protein Interactions / Year: 1982
Title: Lipid-Protein Interactions in a Bacteriochlorophyll-Containing Protein
Authors: Matthews, B.W.
#4: Journal: Acc.Chem.Res. / Year: 1980
Title: Structure of a Green Bacteriochlorophyll Protein
Authors: Matthews, B.W. / Fenna, R.E.
#5: Journal: J.Mol.Biol. / Year: 1979
Title: Structure of a Bacteriochlorophyll A-Protein from the Green Photosynthetic Bacterium Prosthecochloris Aestuarii
Authors: Matthews, B.W. / Fenna, R.E. / Bolognesi, M.C. / Schmid, M.F. / Olson, J.M.
#6: Journal: The Photosynthetic Bacteria / Year: 1978
Title: Bacteriochlorophyll A-Protein from Green Bacteria
Authors: Olson, J.M.
#7: Journal: Biochem.Biophys.Res.Commun. / Year: 1977
Title: Atomic Coordinates for the Chlorophyll Core of a Bacteriochlorophyll A-Protein from Green Photosynthetic Bacteria
Authors: Fenna, R.E. / Ten Eyck, L.F. / Matthews, B.W.
#8: Journal: J.Ultrastruct.Res. / Year: 1977
Title: An Evaluation of Electron Micrographs of Bacteriochlorophyll A-Protein Crystals in Terms of the Structure Determined by X-Ray Crystallography
Authors: Matthews, B.W. / Fenna, R.E. / Remington, S.J.
#9: Journal: BROOKHAVEN SYMP.BIOL. / Year: 1976
Title: Structure of a Bacteriochlorophyll A-Protein from Prosthecochloris Aestuarii
Authors: Fenna, R.E. / Matthews, B.W.
#10: Journal: Nature / Year: 1975
Title: Chlorophyll Arrangement in a Bacteriochlorophyll Protein from Chlorobium Limicola
Authors: Fenna, R.E. / Matthews, B.W.
History
DepositionApr 17, 1998Processing site: BNL
SupersessionJul 15, 1998ID: 3BCL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2007Group: Other
Revision 1.2May 29, 2007Group: Other
Revision 1.3Mar 25, 2008Group: Version format compliance
Revision 1.4Dec 18, 2013Group: Other
Revision 1.5Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BACTERIOCHLOROPHYLL A PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6638
Polymers40,2821
Non-polymers6,3817
Water2,198122
1
A: BACTERIOCHLOROPHYLL A PROTEIN
hetero molecules

A: BACTERIOCHLOROPHYLL A PROTEIN
hetero molecules

A: BACTERIOCHLOROPHYLL A PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,98824
Polymers120,8473
Non-polymers19,14221
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Unit cell
Length a, b, c (Å)111.900, 111.900, 98.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-493-

HOH

-
Components

#1: Protein BACTERIOCHLOROPHYLL A PROTEIN / FENNA-MATTHEWS-OLSON PROTEIN / FMO-PROTEIN / BCHL A PROTEIN / BCP


Mass: 40282.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Prosthecochloris aestuarii (bacteria) / Cellular location: LIGHT GATHERING ANTENNA COMPLEX / References: UniProt: P11741
#2: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 9

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 70 %
Crystal growpH: 7.8
Details: PROTEIN CRYSTALLIZES FROM SOLUTION OF 14MG/ML OF PROTEIN IN 10MM TRIS.HCL BUFFER, PH 7.8, AND 1M NACL AND 5% (W/V) NH4 SO4

-
Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: KODAK FILM / Detector: FILM / Details: ADJUSTABLE COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→22.2 Å / Num. obs: 46456 / % possible obs: 73 % / Redundancy: 2.7 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.046

-
Processing

Software
NameVersionClassification
OSCTSTdata collection
ROTAVATAdata reduction
LYNNTEN EYCK'S NEWREFmodel building
TNT4Crefinement
OSCTSTdata reduction
CCP4(ROTAVATA)data scaling
NEWREF(LYNN TEN EYCK)phasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→20 Å / Stereochemistry target values: TNT PROTGEO V1.0
RfactorNum. reflection% reflection
all0.178 45335 -
obs0.178 45335 79 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 212.3 Å2 / ksol: 0.826 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2720 0 462 122 3304
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.02133060.8
X-RAY DIFFRACTIONt_angle_deg3.34745531.1
X-RAY DIFFRACTIONt_dihedral_angle_d19.2217880
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0231001
X-RAY DIFFRACTIONt_gen_planes0.0244503
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.022810

+
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