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- PDB-3eni: Crystal structure of the Fenna-Matthews-Olson Protein from Chloro... -

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Basic information

Entry
Database: PDB / ID: 3eni
TitleCrystal structure of the Fenna-Matthews-Olson Protein from Chlorobaculum Tepidum
ComponentsBacteriochlorophyll a protein
KeywordsPHOTOSYNTHESIS / BETA SHEET / GAMMA TURN / 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 / Bacteriochlorophyll a protein
Similarity search - Component
Biological speciesChlorobaculum tepidum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTronrud, D. / Camara-Artigas, A. / Blankenship, R. / Allen, J.P.
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: Photosynth.Res. / Year: 2003
Title: The Structure of the Fmo Protein from Chlorobium Tepidum at 2.2 A Resolution
Authors: Camara-Artigas, A. / Blankenship, R. / Allen, J.P.
#2: Journal: J.Mol.Biol. / Year: 1997
Title: Crystal Structure of the Bacteriochlorophyll a Protein from Chlorobium Tepidum
Authors: Li, Y.F. / Zhou, W.L. / Blankenship, R.E. / Allen, J.P.
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionMay 12, 2009ID: 1M50, 1KSA
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_alt_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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
C: Bacteriochlorophyll a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,00918
Polymers80,4242
Non-polymers14,58416
Water3,711206
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)142,51327
Polymers120,6373
Non-polymers21,87624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area51530 Å2
ΔGint-380 kcal/mol
Surface area37260 Å2
MethodPISA
2
C: Bacteriochlorophyll a protein
hetero molecules

C: Bacteriochlorophyll a protein
hetero molecules

C: Bacteriochlorophyll a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,51327
Polymers120,6373
Non-polymers21,87624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area51530 Å2
ΔGint-374 kcal/mol
Surface area37170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.100, 169.100, 169.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein Bacteriochlorophyll a protein / BChl a protein / BCP / Fenna-Matthews-Olson protein / FMO protein


Mass: 40212.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: This species was formerly known as Chlorobium tepidum
Source: (natural) Chlorobaculum tepidum (bacteria) / References: UniProt: Q46393
#2: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 6% (W/V) POLYETHYLENE GLYCOL 600, 50 MM SODIUM CITRATE, 10% (V/V) 2-PROPONAL, pH 5.60, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 15, 1998 / Details: GRAPHITE FILTER
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. all: 41641 / Num. obs: 41641 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 27.796 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 5
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.742 / % possible all: 63.2

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHASERphasing
BUSTER-TNT2.1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2068 1853 5.05 %RANDOM
Rwork0.1633 ---
all0.1655 36706 --
obs0.1655 36706 86.54 %-
Displacement parametersBiso mean: 29.49 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5445 0 1122 206 6773
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01168652
X-RAY DIFFRACTIONt_angle_deg1.19596292
X-RAY DIFFRACTIONt_dihedral_angle_d18.47813710
X-RAY DIFFRACTIONt_pseud_angle17.955360
X-RAY DIFFRACTIONt_trig_c_planes0.0082572
X-RAY DIFFRACTIONt_gen_planes0.0189225
X-RAY DIFFRACTIONt_it1.437686120
X-RAY DIFFRACTIONt_nbd0.045365
LS refinement shellResolution: 2.2→2.33 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3364 225 5.43 %
Rwork0.2705 3922 -
all0.274 4147 -
obs-4147 86.54 %

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