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- PDB-3v3z: I(L177)H mutant structure of photosynthetic reaction center from ... -

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Basic information

Entry
Database: PDB / ID: 3v3z
TitleI(L177)H mutant structure of photosynthetic reaction center from Rhodobacter sphaeroides
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 / : / HEPTANE-1,2,3-TRIOL / : / PHOSPHATE ION / SPEROIDENONE / UBIQUINONE-10 / Reaction center protein H chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / 1,4-DIETHYLENE DIOXIDE / : / HEPTANE-1,2,3-TRIOL / : / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.ptnr2_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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)101,56130
Polymers91,4413
Non-polymers10,11927
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38380 Å2
ΔGint-243 kcal/mol
Surface area29980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.130, 140.130, 186.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: pREHD-I(L177)H / 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: 31385.404 Da / Num. of mol.: 1 / Mutation: I177H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: pufL / Plasmid: pREHD-I(L177)H / 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: pREHD-I(L177)H / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): DD13 / References: UniProt: P0C0Y9

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Non-polymers , 12 types, 76 molecules

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


Mass: 229.402 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H16O3
#7: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#9: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


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


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


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


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


Mass: 594.993 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H70O2
#14: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 49 / 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: 5.77 Å3/Da / Density % sol: 78.67 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 24, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2.9→28.9 Å / Num. all: 47384 / Num. obs: 45707 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.61 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.25
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.55 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 2.3 / % possible all: 90.2

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E6D

1e6d


Resolution: 2.9→28.9 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 13.174 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.424 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25063 2286 5 %RANDOM
Rwork0.20394 ---
all0.212 45707 --
obs0.20626 43421 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.052 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20.69 Å20 Å2
2--1.39 Å20 Å2
3----2.08 Å2
Refinement stepCycle: LAST / Resolution: 2.9→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6484 0 683 49 7216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227422
X-RAY DIFFRACTIONr_angle_refined_deg1.722.03410160
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6395821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87922.624282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3515969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7431531
X-RAY DIFFRACTIONr_chiral_restr0.0860.21022
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215634
X-RAY DIFFRACTIONr_mcbond_it0.4681.54075
X-RAY DIFFRACTIONr_mcangle_it0.89626515
X-RAY DIFFRACTIONr_scbond_it1.05633347
X-RAY DIFFRACTIONr_scangle_it1.8624.53645
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 154 -
Rwork0.354 2912 -
obs--100 %

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