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- PDB-3zuw: Photosynthetic Reaction Centre Mutant with TYR L128 replaced with HIS -

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Basic information

Entry
Database: PDB / ID: 3zuw
TitlePhotosynthetic Reaction Centre Mutant with TYR L128 replaced with HIS
Components(REACTION CENTER PROTEIN ...) x 3
KeywordsPHOTOSYNTHESIS / ELECTRON TRANSFER / PRIMARY CHARGE SEPARATION / CHARGE RECOMBINATION / TRANSIENT ABSORPTION SPECTROSCOPY
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 / : / 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: 2.31 Å
AuthorsGibasiewicz, K. / Pajzderska, M. / Potter, J.A. / Fyfe, P.K. / Dobek, A. / Brettel, K. / Jones, M.R.
CitationJournal: J Phys Chem B / Year: 2011
Title: Mechanism of Recombination of the P(+)H(A)(-) Radical Pair in Mutant Rhodobacter Sphaeroides Reaction Centers with Modified Free Energy Gaps between P(+)B(A)(-) and P(+)H(A)(-).
Authors: Gibasiewicz, K. / Pajzderska, M. / Potter, J.A. / Fyfe, P.K. / Dobek, A. / Brettel, K. / Jones, M.R.
History
DepositionJul 20, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Advisory / Data collection / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.method
Revision 1.2May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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)103,84324
Polymers93,7863
Non-polymers10,05721
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38600 Å2
ΔGint-206.4 kcal/mol
Surface area28670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.865, 139.865, 184.738
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-2056-

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 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) / Production host: RHODOBACTER SPHAEROIDES (bacteria) / References: UniProt: P0C0Y7
#2: Protein REACTION CENTER PROTEIN L CHAIN / PHOTOSYNTHETIC REACTION CENTER L SUBUNIT


Mass: 31321.361 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Production host: RHODOBACTER SPHAEROIDES (bacteria) / References: UniProt: P0C0Y8
#3: Protein REACTION CENTER PROTEIN M CHAIN / PHOTOSYNTHETIC REACTION CENTER M SUBUNIT


Mass: 34398.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Production host: RHODOBACTER SPHAEROIDES (bacteria) / References: UniProt: P0C0Y9

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Non-polymers , 8 types, 319 molecules

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


Mass: 229.402 Da / Num. of mol.: 9 / 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-FE / FE (III) ION


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


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


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


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN L, TYR 129 TO HIS
Sequence detailsRESIDUE L128 HAS BEEN MUTATED TO HIS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.73 Å3/Da / Density % sol: 78.6 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop
Details: VAPOUR DIFFUSION, SITTING DROP, 0.09% LDAO, 3.5% 1,2,3 HEPTANETRIOL, 0.75M POTASSIUM PHOSPHATE PH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.3→17.9 Å / Num. obs: 85153 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 43.5 Å2 / Rmerge(I) obs: 0.07

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→17.87 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.484 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 4476 5 %RANDOM
Rwork0.19176 ---
obs0.19338 85153 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.001 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20.49 Å20 Å2
2--0.98 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.31→17.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6468 0 684 298 7450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0227413
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1412.03410140
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8545820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4422.598281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64115972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.361532
X-RAY DIFFRACTIONr_chiral_restr0.1610.21014
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0215624
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5041.54071
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.52326509
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.89233342
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.474.53631
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: 2.311→2.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 302 -
Rwork0.265 5791 -
obs--92.4 %

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