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- PDB-1jgy: Photosynthetic Reaction Center Mutant With Tyr M 76 Replaced With Phe -

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Basic information

Entry
Database: PDB / ID: 1jgy
TitlePhotosynthetic Reaction Center Mutant With Tyr M 76 Replaced With Phe
Components(Photosynthetic Reaction Center ...) x 3
KeywordsPHOTOSYNTHESIS / alpha helix
Function / homology
Function and homology information


: / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / photosynthetic electron transport in photosystem II / 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 / CARDIOLIPIN / : / SPHEROIDENE / UBIQUINONE-10 / Reaction center protein M chain / Reaction center protein L chain / Reaction center protein H chain / Reaction center protein L chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / : / SPHEROIDENE / 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: 2.7 Å
AuthorsCamara-Artigas, A. / Magee, C.L. / Williams, J.C. / Allen, J.P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Individual interactions influence the crystalline order for membrane proteins.
Authors: Camara-Artigas, A. / Magee, C.L. / Williams, J.C. / Allen, J.P.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Specific Alteration of the Oxidation Potential of the Electron Donor in Reaction Centers from Rhodobacter sphaeroides
Authors: Lin, X. / Murchison, H.A. / Nagarajan, V. / Parson, W.W. / Allen, J.P. / Willians, J.C.
History
DepositionJun 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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 / _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
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Photosynthetic Reaction Center L Subunit
M: Photosynthetic Reaction Center M Subunit
H: Photosynthetic Reaction Center H Subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,17213
Polymers93,7953
Non-polymers8,37710
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31520 Å2
ΔGint-227 kcal/mol
Surface area29810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.680, 141.680, 186.840
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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Photosynthetic Reaction Center ... , 3 types, 3 molecules LMH

#1: Protein Photosynthetic Reaction Center L Subunit / reaction center protein L chain


Mass: 31346.389 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Species (production host): Rhodobacter sphaeroides / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / Strain (production host): 2.4.1 / References: UniProt: P02954, UniProt: P0C0Y8*PLUS
#2: Protein Photosynthetic Reaction Center M Subunit / reaction center protein M chain


Mass: 34382.543 Da / Num. of mol.: 1 / Mutation: Y76F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Species (production host): Rhodobacter sphaeroides / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / Strain (production host): 2.4.1 / References: UniProt: P02953, UniProt: P0C0Y9*PLUS
#3: Protein Photosynthetic Reaction Center H Subunit / reaction center protein H chain


Mass: 28066.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Species (production host): Rhodobacter sphaeroides / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / Strain (production host): 2.4.1 / References: UniProt: P11846, UniProt: P0C0Y7*PLUS

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Non-polymers , 7 types, 99 molecules

#4: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


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


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#7: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4
#8: Chemical ChemComp-SPO / SPHEROIDENE


Mass: 568.914 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H60O
#9: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Potasium phosphate, LDAO, heptane triol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.08 %LDAO1drop
30.75 Mpotassium phosphate1drop
43.5 %heptanetriol1drop
51.6 Mpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 11, 2000
Details: 58 cm long, Pt-coated, fused silica, vertical focusmirror
RadiationMonochromator: Cyclindrically bent triangular Si(111) asymmetric cut, horizontal focus monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 35678 / Num. obs: 35678 / % possible obs: 59.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.103
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.21 / % possible all: 38.05
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 75641
Reflection shell
*PLUS
% possible obs: 38.7 % / Rmerge(I) obs: 0.21

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qov

1qov


Resolution: 2.7→29.1 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3097015.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 3781 10.1 %RANDOM
Rwork0.218 ---
all-60002 --
obs-37579 62.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.84 Å2 / ksol: 0.2822 e/Å3
Displacement parametersBiso mean: 49.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.46 Å21.91 Å20 Å2
2--2.46 Å20 Å2
3----4.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.43 Å
Luzzati d res low-3 Å
Luzzati sigma a0.55 Å0.72 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6468 0 566 89 7123
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.952
X-RAY DIFFRACTIONc_scbond_it1.412
X-RAY DIFFRACTIONc_scangle_it2.252.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 517 10.5 %
Rwork0.346 4410 -
obs--50 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4RC_ANA.PARRC_ANA.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.1 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 49.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.375 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.346

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