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- PDB-3eoj: Fmo protein from Prosthecochloris Aestuarii 2K AT 1.3A Resolution -

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Basic information

Entry
Database: PDB / ID: 3eoj
TitleFmo protein from Prosthecochloris Aestuarii 2K AT 1.3A Resolution
ComponentsBacteriochlorophyll a protein
KeywordsPHOTOSYNTHESIS / EXCITATION ENERGY TRANSFER / BETA SHEET / GAMMA-TURNS / Bacteriochlorophyll / Chlorophyll / Chromophore / Electron transport / Magnesium / Metal-binding / Reaction center / Transport
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 / AMMONIUM ION / Bacteriochlorophyll a protein
Similarity search - Component
Biological speciesProsthecochloris aestuarii 2K (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsTronrud, D.E. / Wen, J. / Gay, L. / Blankenship, R.E.
Citation
Journal: Photosynth.Res. / Year: 2009
Title: The structural basis for the difference in absorbance spectra for the FMO antenna protein from various green sulfur bacteria.
Authors: Tronrud, D.E. / Wen, J. / Gay, L. / Blankenship, R.E.
#1: Journal: The 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.
#2: 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.
#3: Journal: Chem.Scr. / Year: 1983
Title: Structural Studies of a Bacteriochlorophyll-Containing Protein
Authors: Schmid, M.F. / Tronrud, D.E. / Matthews, B.W.
#4: Journal: Lipid-Protein Interactions / Year: 1982
Title: Lipid-Protein Interactions in a Bacteriochlorophyll-Containing Protein
Authors: Matthews, B.W.
#5: Journal: Acc.Chem.Res. / Year: 1980
Title: Structure of a Green Bacteriochlorophyll Protein
Authors: Matthews, B.W. / Fenna, R.E.
#6: 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.
#7: Journal: The Photosynthetic Bacteria / Year: 1978
Title: Bacteriochlorophyll A-Protein from Green Bacteria
Authors: Olson, J.M.
#8: 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.
#9: 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.
#10: Journal: Brookhaven Symp.Biol. / Year: 1976
Title: Structure of a Bacteriochlorophyll A-Protein from Prosthecochloris Aestuarii
Authors: Fenna, R.E. / Matthews, B.W.
#11: Journal: Nature / Year: 1975
Title: Chlorophyll Arrangement in a Bacteriochlorophyll Protein from Chlorobium Limicola
Authors: Fenna, R.E. / Matthews, B.W.
History
DepositionSep 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 18, 2013Group: Other
Revision 1.3Sep 6, 2023Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: Bacteriochlorophyll a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,54626
Polymers40,2821
Non-polymers8,26425
Water7,314406
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)145,63978
Polymers120,8473
Non-polymers24,79275
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area54470 Å2
ΔGint-211 kcal/mol
Surface area38880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.242, 111.242, 98.198
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-2378-

NH4

21A-1155-

HOH

31A-1200-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bacteriochlorophyll a protein / BChl a protein / BCP / FENNA-MATTHEWS-OLSON protein / FMO protein


Mass: 40282.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ANTENNA COMPLEX / Source: (natural) Prosthecochloris aestuarii 2K (bacteria) / References: UniProt: P11741

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Non-polymers , 5 types, 431 molecules

#2: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsACCORDING TO THE AUTHORS THE DATABASE SEQUENCE IS IN ERROR

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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

CrystalDensity Matthews: 4.35 Å3/Da / Density % sol: 71.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Well Solution: 10mM Tris/HCL pH 8.0, 1.0M NaCl, 10% w/v (NH4)2SO4. Protein Solution: 10mM Tris/HCL pH 7.8 1.0M NaCl at 14mg/ml of complex. Drop composed of 5ul of protein solution and 3ul of ...Details: Well Solution: 10mM Tris/HCL pH 8.0, 1.0M NaCl, 10% w/v (NH4)2SO4. Protein Solution: 10mM Tris/HCL pH 7.8 1.0M NaCl at 14mg/ml of complex. Drop composed of 5ul of protein solution and 3ul of well solution., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 23, 2007 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.3→50 Å / Num. all: 168292 / Num. obs: 168292 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 26.5
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.77 / Num. unique all: 16812 / % possible all: 100

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Processing

Software
NameClassification
ARP/wARPmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BCL

1bcl
PDB Unreleased entry


Resolution: 1.3→50 Å / Num. parameters: 37346 / Num. restraintsaints: 52424 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE. THE BOND LENGTHS AND ANGLES OF ALL BCL MOLECULES, EXCEPT FOR 378, WERE RESTRAINED TO THE GROUP AVERAGES CALCULATED FROM THESE SEVEN MOLECULES. ...Details: WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE. THE BOND LENGTHS AND ANGLES OF ALL BCL MOLECULES, EXCEPT FOR 378, WERE RESTRAINED TO THE GROUP AVERAGES CALCULATED FROM THESE SEVEN MOLECULES. NO EXTERNAL LIBRARY WAS USED. THE BOND LENGTHS AND ANGLES OF 378 WERE RESTRAINED TO THE AVERAGE VALUES OF THE OTHER SEVEN BCL MOLECULES
RfactorNum. reflection% reflectionSelection details
Rfree0.1613 8438 5.28 %RANDOM
Rwork0.1353 ---
all0.1365 168283 --
obs0.1365 168283 94.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Bsol: 3.31935 Å2 / ksol: 0.8587 e/Å3
Displacement parametersBiso mean: 16.78 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeNum. disordered residues: 125 / Occupancy sum hydrogen: 3115.1 / Occupancy sum non hydrogen: 3629.76
Refinement stepCycle: LAST / Resolution: 1.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 571 406 3722
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0311
X-RAY DIFFRACTIONs_zero_chiral_vol0.07
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.078
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.03
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.032
X-RAY DIFFRACTIONs_approx_iso_adps0.093
LS refinement shellResolution: 1.3→1.35 Å
RfactorNum. reflection% reflection
Rfree0.254 871 -
Rwork0.2319 --
obs-17522 97 %

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