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- PDB-3bsd: Light harvesting protein from RC of Chlorobium tepidum -

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Basic information

Entry
Database: PDB / ID: 3bsd
TitleLight harvesting protein from RC of Chlorobium tepidum
ComponentsBacteriochlorophyll a protein
KeywordsPHOTOSYNTHESIS / green bacteria / light harvesting / 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 / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsNelson, N. / Frolow, F. / Brn-Shem, A.
CitationJournal: Febs Lett. / Year: 2004
Title: Evolution of photosystem I - from symmetry through pseudo-symmetry to asymmetry.
Authors: Ben-Shem, A. / Frolow, F. / Nelson, N.
History
DepositionDec 23, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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_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.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_comp_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.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_comp_id / _struct_conn.ptnr2_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,66010
Polymers40,3431
Non-polymers7,3169
Water3,207178
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)142,97930
Polymers121,0303
Non-polymers21,94927
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_466y-1/2,-z+3/2,-x+11
crystal symmetry operation8_656-z+1,x+1/2,-y+3/21
Buried area52080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.695, 167.695, 167.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-427-

HOH

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Components

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


Mass: 40343.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlorobaculum tepidum (bacteria) / References: UniProt: Q46393
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPUTATIVE ADDITIONAL CHLOROPHYLL BINDING SITE

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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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.6M hexanediol, 0.2M magnesium chloride, 0.1M HEPES pH 7.5, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 28, 1999 / Details: Osmic multilayer mirrors
RadiationMonochromator: Osmic multilayer mirrors that act also as a monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→118.68 Å / Num. all: 18219 / Num. obs: 18207 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 24.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1780 / Rsym value: 0.64 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0013refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4BCL

4bcl


Resolution: 2.3→44.82 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.917 / SU B: 20.669 / SU ML: 0.257 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.427 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27328 920 5.1 %RANDOM
Rwork0.17363 ---
obs0.17838 18174 99.7 %-
all-18174 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.462 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 505 178 3481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213439
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.3092.1384782
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6295358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.75623.529136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.16915461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.851522
X-RAY DIFFRACTIONr_chiral_restr0.1240.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022572
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2430.21687
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22177
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2191
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.2127
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.228
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.63821821
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.70332858
X-RAY DIFFRACTIONr_scbond_it2.74721829
X-RAY DIFFRACTIONr_scangle_it3.46631908
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 52 -
Rwork0.247 1246 -
obs--99.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.857-0.87850.45292.350.34741.96310.32260.6855-0.3768-0.5427-0.2710.09020.00490.097-0.0516-0.04850.1737-0.08290.0877-0.2147-0.154837.794112.946109.579
21.4396-1.05960.59711.5274-0.34341.20460.26140.6805-0.2202-0.4052-0.34880.1899-0.02030.06720.08740.00840.147-0.05890.1991-0.1509-0.151636.344118.109109.638
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 3668 - 366
2X-RAY DIFFRACTION2AC3671
3X-RAY DIFFRACTION2AD3681
4X-RAY DIFFRACTION2AE3691
5X-RAY DIFFRACTION2AF3701
6X-RAY DIFFRACTION2AG3711
7X-RAY DIFFRACTION2AH3721
8X-RAY DIFFRACTION2AI3731
9X-RAY DIFFRACTION2AJ4001
10X-RAY DIFFRACTION2AB3741

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