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- PDB-2boz: Photosynthetic Reaction Center Mutant With Gly M203 Replaced With Leu -

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Basic information

Entry
Database: PDB / ID: 2boz
TitlePhotosynthetic Reaction Center Mutant With Gly M203 Replaced With Leu
Components(REACTION CENTER PROTEIN ...Photosynthetic reaction centre) x 3
KeywordsPHOTOSYNTHESIS / CARDIOLIPIN / ELECTRON TRANSPORT / MEMBRANE PROTEIN / REACTION CENTER
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 / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / membrane => GO:0016020 / metal ion binding
Similarity search - Function
Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / 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, subunit M; domain 1 / Photosystem II protein D1-like / Photosynthetic Reaction Center; Chain H, domain 2 / Photosynthetic Reaction Center, subunit H, domain 2 / Photosynthetic Reaction Center; Chain H, domain 1 / Photosynthetic reaction centre, H subunit, N-terminal domain / 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 centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / 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 / DECANE / : / PHOSPHATE ION / SPEROIDENONE / UBIQUINONE-10 / Reaction center protein M chain / Reaction center protein L chain / Reaction center protein H chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / DECANE / : / PHOSPHATE ION / SPEROIDENONE / UBIQUINONE-10 / Reaction center protein M chain / Reaction center protein L chain / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Reaction center protein H chain
Similarity search - Component
Biological speciesRHODOBACTER SPHAEROIDES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPotter, J.P. / Fyfe, P.K. / Jones, M.R.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Strong Effects of an Individual Water Molecule on the Rate of Light-Driven Charge Separation in the Rhodobacter Sphaeroides Reaction Center.
Authors: Potter, J.A. / Fyfe, P.K. / Frolov, D. / Wakeham, M.C. / Van Grondelle, R. / Robert, B. / Jones, M.R.
#1: Journal: Biochemistry / Year: 2000
Title: Structural Consequences of the Replacement of Glycine M203 with Aspartic Acid in the Reaction Center from Rhodobacter Sphaeroides
Authors: Fyfe, P.K. / Ridge, J.P. / Mcauley, K.E. / Cogdell, R.J. / Isaacs, N.W. / Jones, M.R.
History
DepositionApr 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 20, 2013Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)103,20422
Polymers93,8673
Non-polymers9,33619
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36900 Å2
ΔGint-215.8 kcal/mol
Surface area28590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.613, 138.613, 185.274
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11H-2054-

HOH

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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 centre / PHOTOSYNTHETIC REACTION CENTER H SUBUNIT


Mass: 28066.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Plasmid: PRKEH10D / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): GM203L / References: UniProt: P11846, UniProt: P0C0Y7*PLUS
#2: Protein REACTION CENTER PROTEIN L CHAIN / Photosynthetic reaction centre / PHOTOSYNTHETIC REACTION CENTER L SUBUNIT


Mass: 31346.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Plasmid: PRKEH10D / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): GM203L / References: UniProt: P02954, UniProt: P0C0Y8*PLUS
#3: Protein REACTION CENTER PROTEIN M CHAIN / Photosynthetic reaction centre / PHOTOSYNTHETIC REACTION CENTER M SUBUNIT


Mass: 34454.648 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Plasmid: PRKEH10D / Production host: RHODOBACTER SPHAEROIDES (bacteria) / Strain (production host): GM203L / References: UniProt: P02953, UniProt: P0C0Y9*PLUS

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Non-polymers , 9 types, 387 molecules

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


Mass: 229.402 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Chemical ChemComp-D10 / DECANE / Decane


Mass: 142.282 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22
#6: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


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


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


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#9: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#10: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#11: Chemical ChemComp-SPN / SPEROIDENONE


Mass: 594.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H70O2
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN H, GLY 203 TO LEU

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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: 4.91 Å3/Da / Density % sol: 74.75 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 0.977
DetectorType: ADSC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.4→18 Å / Num. obs: 80240 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILD-TYPE RHODOBACTER SPHAEROIDES UNPUBLISHED DATA

Resolution: 2.4→17.96 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.262 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 3991 5 %RANDOM
Rwork0.174 ---
obs0.175 76249 99.5 %-
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: 36.29 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20.61 Å20 Å2
2--1.22 Å20 Å2
3----1.83 Å2
Refinement stepCycle: LAST / Resolution: 2.4→17.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6475 0 632 368 7475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0227352
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8812.01910072
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6985820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92622.643280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.2615971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3681531
X-RAY DIFFRACTIONr_chiral_restr0.2150.21018
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025638
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.23797
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2532
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9061.54185
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45426513
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.40233871
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3034.53549
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 302
Rwork0.255 5408
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)
10.91630.1431-0.46590.5565-0.1821.0138-0.01510.0481-0.0724-0.10140.0029-0.1124-0.0066-0.01560.0122-0.21140.03050.034-0.16520.0017-0.169165.31253.64260.736
21.01820.0658-0.25530.5417-0.21211.09110.08980.15260.2348-0.04420.00820.0294-0.2667-0.1467-0.098-0.13510.11540.0635-0.13730.0365-0.149156.15273.19859.313
30.730.2812-0.04020.8785-0.00110.73080.0734-0.0481-0.05520.0325-0.01360.0784-0.0095-0.123-0.0598-0.14140.05720.024-0.00290.0201-0.12141.63649.54577.965
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 281
2X-RAY DIFFRACTION2M1 - 302
3X-RAY DIFFRACTION3H11 - 250

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