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- PDB-3vdi: Structure of the FMO protein from Pelodictyon phaeum -

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Basic information

Entry
Database: PDB / ID: 3vdi
TitleStructure of the FMO protein from Pelodictyon phaeum
Componentsbacteriochlorophyll A proteinBacteriochlorophyll
KeywordsPHOTOSYNTHESIS / alpha/beta protein / energy transfer
Function / homologyBacteriochlorophyll-a Protein / Bacteriochlorophyll A / Clam / Mainly Beta / BACTERIOCHLOROPHYLL A
Function and homology information
Biological speciesPelodictyon phaeum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsTronrud, D.E. / Larson, C.R. / Seng, C.O. / Lauman, L. / Matthies, H.J. / Wen, J. / Blankenship, R.E. / Allen, J.P.
Citation
Journal: Photosynth.Res. / Year: 2012
Title: Reinterpretation of the electron density at the site of the eighth bacteriochlorophyll in the FMO protein from Pelodictyon phaeum.
Authors: Tronrud, D.E. / Allen, J.P.
#1: Journal: Photosynth.Res. / Year: 2011
Title: The Three-Dimensional Structure of the Fmo Protein from Pelodictyon Phaeum and the Implications for Energy Transfer.
Authors: Larson, C.R. / Seng, C.O. / Lauman, L. / Matthies, H.J. / Wen, J. / Blankenship, R.E. / Allen, J.P.
History
DepositionJan 5, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionJan 25, 2012ID: 3OEG
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2May 9, 2012Group: Database references
Revision 1.3Sep 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)47,77712
Polymers40,6201
Non-polymers7,15711
Water3,657203
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)143,33236
Polymers121,8593
Non-polymers21,47233
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area53560 Å2
ΔGint-271 kcal/mol
Surface area37520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.967, 83.967, 115.724
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-1137-

HOH

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Components

#1: Protein bacteriochlorophyll A protein / Bacteriochlorophyll


Mass: 40619.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pelodictyon phaeum (bacteria)
#2: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


Mass: 911.504 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 mM HEPES, pH 7.5, 16% PEG2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 1, 2009
RadiationMonochromator: horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.99→48 Å / Num. all: 29980 / Num. obs: 29980 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 7.7 % / Biso Wilson estimate: 23.02 Å2 / Rmerge(I) obs: 0.186
Reflection shellResolution: 1.99→2.05 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.2 / % possible all: 94

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EOJ

3eoj


Resolution: 1.99→40 Å / Cor.coef. Fo:Fc: 0.9465 / Cor.coef. Fo:Fc free: 0.9375 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1902 1523 5.08 %RANDOM
Rwork0.1621 ---
all0.1635 31719 --
obs0.1635 29980 --
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.3388 Å20 Å20 Å2
2--1.3388 Å20 Å2
3----2.6777 Å2
Refine analyzeLuzzati coordinate error obs: 0.174 Å
Refinement stepCycle: LAST / Resolution: 1.99→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2767 0 500 203 3470
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1156SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes122HARMONIC2
X-RAY DIFFRACTIONt_gen_planes457HARMONIC5
X-RAY DIFFRACTIONt_it3405HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion410SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3711SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3405HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4707HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.74
X-RAY DIFFRACTIONt_other_torsion14.32
LS refinement shellResolution: 1.99→2.06 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2132 148 5.47 %
Rwork0.1776 2556 -
all0.1797 2704 -
Refinement TLS params.Method: refined / Origin x: -24.1847 Å / Origin y: 34.0687 Å / Origin z: 24.3031 Å
111213212223313233
T-0.0188 Å2-0.0189 Å2-0.0188 Å2-0.0158 Å20.028 Å2---0.0721 Å2
L0.2839 °2-0.0133 °2-0.044 °2-0.2971 °2-0.0071 °2--0.4019 °2
S-0.045 Å °-0.0019 Å °0.059 Å °0.007 Å °-0.0292 Å °-0.081 Å °-0.0533 Å °0.0898 Å °0.0741 Å °
Refinement TLS groupSelection details: {A|*}

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