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- PDB-3v3y: Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV -

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Basic information

Entry
Database: PDB / ID: 3v3y
TitlePhotosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV
Components(Reaction center protein ...) x 3
KeywordsELECTRON TRANSPORT / Photosynthetic reaction center / Primary electron donor / membrane
Function / homology
Function and homology information


plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / : / photosynthesis, light reaction / metal ion binding
Similarity search - Function
Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal ...Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / 1,4-DIETHYLENE DIOXIDE / : / PHOSPHATE ION / SPEROIDENONE / UBIQUINONE-10 / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsGabdulkhakov, A.G. / Fufina, T.Y. / Vasilieva, L.G. / Shuvalov, V.A.
CitationJournal: Biochim.Biophys.Acta / Year: 2012
Title: The site-directed mutation I(L177)H in Rhodobacter sphaeroides reaction center affects coordination of P(A) and B(B) bacteriochlorophylls.
Authors: Vasilieva, L.G. / Fufina, T.Y. / Gabdulkhakov, A.G. / Leonova, M.M. / Khatypov, R.A. / Shuvalov, V.A.
History
DepositionDec 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Sep 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 / 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_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.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
H: Reaction center protein H chain
L: Reaction center protein L chain
M: Reaction center protein M chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,63828
Polymers91,4163
Non-polymers10,22225
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38410 Å2
ΔGint-237 kcal/mol
Surface area29250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.750, 139.750, 185.604
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Detailsheterotrimer

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Components

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Reaction center protein ... , 3 types, 3 molecules HLM

#1: Protein Reaction center protein H chain / Photosynthetic reaction center H subunit


Mass: 26170.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: puhA / Plasmid: pREH-D2 L177 / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): DD13 / References: UniProt: P0C0Y7
#2: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 31360.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufL / Plasmid: pREH-D2 L177 / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): DD13 / References: UniProt: P0C0Y8
#3: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 33885.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufM / Plasmid: pREH-D2 L177 / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): DD13 / References: UniProt: P0C0Y9

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Non-polymers , 10 types, 117 molecules

#4: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#6: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#7: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#8: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8O2
#9: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#10: Chemical ChemComp-SPN / SPEROIDENONE


Mass: 594.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H70O2
#11: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#12: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THE DISCREPANCY IS ASSOCIATED TO A DIFFERENT STRAIN SEQUENCE (STRAIN RV)

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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: 5.72 Å3/Da / Density % sol: 78.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 3.5% 1,2,3 -heptanetriol, 2% dioxane, 0.1% LDAO, 1M potassium phosphate , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Nov 11, 2011
RadiationMonochromator: Montel 200 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.8→26.6 Å / Num. all: 52181 / Num. obs: 51787 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.75 % / Rmerge(I) obs: 0.185 / Net I/σ(I): 6.11
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.91 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 1.7 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E6D

1e6d


Resolution: 2.8→19.941 Å / SU ML: 0.9 / σ(F): 0 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2640 5.11 %RANDOM
Rwork0.244 ---
all0.2465 51787 --
obs0.246 51655 99.42 %-
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 11.091 Å2 / ksol: 0.274 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9515 Å2-0 Å2-0 Å2
2--1.9515 Å2-0 Å2
3----3.903 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6482 0 696 92 7270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017431
X-RAY DIFFRACTIONf_angle_d1.74210164
X-RAY DIFFRACTIONf_dihedral_angle_d20.0262710
X-RAY DIFFRACTIONf_chiral_restr0.091016
X-RAY DIFFRACTIONf_plane_restr0.0061228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.85080.37161340.31592537X-RAY DIFFRACTION99
2.8508-2.90550.33151510.28152543X-RAY DIFFRACTION100
2.9055-2.96460.32451380.27672550X-RAY DIFFRACTION100
2.9646-3.02890.32051450.27192542X-RAY DIFFRACTION100
3.0289-3.09910.29921290.27672592X-RAY DIFFRACTION99
3.0991-3.17630.3491540.28082535X-RAY DIFFRACTION100
3.1763-3.26180.33331380.27712553X-RAY DIFFRACTION100
3.2618-3.35730.30141240.28782578X-RAY DIFFRACTION99
3.3573-3.46520.38811480.27862554X-RAY DIFFRACTION100
3.4652-3.58830.3531520.27892555X-RAY DIFFRACTION100
3.5883-3.73110.27621320.26482555X-RAY DIFFRACTION99
3.7311-3.89970.2711530.24932543X-RAY DIFFRACTION99
3.8997-4.10360.30361250.24942582X-RAY DIFFRACTION99
4.1036-4.35820.29341420.23232571X-RAY DIFFRACTION99
4.3582-4.69070.22411250.21532581X-RAY DIFFRACTION99
4.6907-5.15530.23031390.20242613X-RAY DIFFRACTION99
5.1553-5.88450.2471290.21172620X-RAY DIFFRACTION100
5.8845-7.35160.22221440.1962660X-RAY DIFFRACTION100
7.3516-19.94180.21761380.20362751X-RAY DIFFRACTION100

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