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- PDB-4bcl: FMO protein from Prosthecochloris aestuarii 2K at Room Temperature -

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Basic information

Entry
Database: PDB / ID: 4bcl
TitleFMO protein from Prosthecochloris aestuarii 2K at Room Temperature
ComponentsBACTERIOCHLOROPHYLL A PROTEINBacteriochlorophyll
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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Components

#1: Protein BACTERIOCHLOROPHYLL A PROTEIN / Bacteriochlorophyll / 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 / Bacteriochlorophyll


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


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

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Experimental details

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Experiment

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

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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

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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

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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

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