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- PDB-3prc: PHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (QB-... -

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Basic information

Entry
Database: PDB / ID: 3prc
TitlePHOTOSYNTHETIC REACTION CENTER FROM RHODOPSEUDOMONAS VIRIDIS (QB-DEPLETED)
Components(PHOTOSYNTHETIC REACTION ...) x 4
KeywordsPHOTOSYNTHETIC REACTION CENTER / SECONDARY QUINONE (QB)-DEPLETED
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 / photosynthesis / electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosynthetic Reaction Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / 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 Center, subunit C; domain 2 / Photosynthetic Reaction Center, subunit C, domain 2 / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / 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 / Multiheme cytochrome c family profile. / 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 / Multiheme cytochrome superfamily / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Prokaryotic membrane lipoprotein lipid attachment site profile. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL B / BACTERIOPHEOPHYTIN B / : / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE-7 / 15-cis-1,2-dihydroneurosporene / Reaction center protein H chain / Reaction center protein L chain / Reaction center protein M chain / Photosynthetic reaction center cytochrome c subunit
Similarity search - Component
Biological speciesBlastochloris viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.4 Å
AuthorsLancaster, C.R.D. / Michel, H.
Citation
Journal: Structure / Year: 1997
Title: The coupling of light-induced electron transfer and proton uptake as derived from crystal structures of reaction centres from Rhodopseudomonas viridis modified at the binding site of the secondary quinone, QB.
Authors: Lancaster, C.R. / Michel, H.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Refined Crystal Structures of Reaction Centres from Rhodopseudomonas Viridis in Complexes with the Herbicide Atrazine and Two Chiral Atrazine Derivatives Also Lead to a New Model of the Bound Carotenoid
Authors: Lancaster, C.R.D. / Michel, H.
#2: Journal: Biochim.Biophys.Acta / Year: 1998
Title: Ubiquinone Reduction and Protonation in the Reaction Centre of Rhodopseudomonas Viridis: X-Ray Structures and Their Functional Implications
Authors: Lancaster, C.R.D.
#3: Journal: J.Mol.Biol. / Year: 1995
Title: Crystallographic Refinement at 2.3 A Resolution and Refined Model of the Photosynthetic Reaction Centre from Rhodopseudomonas Viridis
Authors: Deisenhofer, J. / Epp, O. / Sinning, I. / Michel, H.
#4: Journal: Science / Year: 1989
Title: The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas Viridis
Authors: Deisenhofer, J. / Michel, H.
#5: Journal: Nature / Year: 1985
Title: Structure of the Protein Subunits in the Photosynthetic Reaction Centre of Rhodopseudomonas Viridis at 3 Angstroms Resolution
Authors: Deisenhofer, J. / Epp, O. / Miki, K. / Huber, R. / Michel, H.
#6: Journal: J.Mol.Biol. / Year: 1984
Title: X-Ray Structure Analysis of a Membrane Protein Complex. Electron Density Map at 3 A Resolution and a Model of the Chromophores of the Photosynthetic Reaction Center from Rhodopseudomonas Viridis
Authors: Deisenhofer, J. / Epp, O. / Miki, K. / Huber, R. / Michel, H.
#7: Journal: J.Mol.Biol. / Year: 1982
Title: Three-Dimensional Crystals of a Membrane Protein Complex. The Photosynthetic Reaction Centre from Rhodopseudomonas Viridis
Authors: Michel, H.
History
DepositionJul 29, 1997Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / 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.process_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 / _software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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
C: PHOTOSYNTHETIC REACTION CENTER
L: PHOTOSYNTHETIC REACTION CENTER
M: PHOTOSYNTHETIC REACTION CENTER
H: PHOTOSYNTHETIC REACTION CENTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,52428
Polymers132,4104
Non-polymers11,11424
Water7,656425
1
C: PHOTOSYNTHETIC REACTION CENTER
L: PHOTOSYNTHETIC REACTION CENTER
M: PHOTOSYNTHETIC REACTION CENTER
H: PHOTOSYNTHETIC REACTION CENTER
hetero molecules

C: PHOTOSYNTHETIC REACTION CENTER
L: PHOTOSYNTHETIC REACTION CENTER
M: PHOTOSYNTHETIC REACTION CENTER
H: PHOTOSYNTHETIC REACTION CENTER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,04756
Polymers264,8198
Non-polymers22,22848
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50350 Å2
ΔGint-413 kcal/mol
Surface area41000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.500, 223.500, 113.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11H-869-

HOH

21H-873-

HOH

31H-901-

HOH

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Components

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PHOTOSYNTHETIC REACTION ... , 4 types, 4 molecules CLMH

#1: Protein PHOTOSYNTHETIC REACTION CENTER / Photosynthetic reaction centre


Mass: 37450.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / Cellular location: INTRACYTOPLASMIC MEMBRANE (ICM) / References: UniProt: P07173
#2: Protein PHOTOSYNTHETIC REACTION CENTER / Photosynthetic reaction centre


Mass: 30469.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / Cellular location: INTRACYTOPLASMIC MEMBRANE (ICM) / References: UniProt: P06009
#3: Protein PHOTOSYNTHETIC REACTION CENTER / Photosynthetic reaction centre


Mass: 35932.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / Cellular location: INTRACYTOPLASMIC MEMBRANE (ICM) / References: UniProt: P06010
#4: Protein PHOTOSYNTHETIC REACTION CENTER / Photosynthetic reaction centre


Mass: 28557.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Blastochloris viridis (bacteria) / Cellular location: INTRACYTOPLASMIC MEMBRANE (ICM) / References: UniProt: P06008

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Non-polymers , 9 types, 449 molecules

#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical
ChemComp-BCB / BACTERIOCHLOROPHYLL B / Bacteriochlorophyll


Mass: 909.488 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H72MgN4O6
#7: Chemical ChemComp-BPB / BACTERIOPHEOPHYTIN B / Pheophytin


Mass: 887.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O6
#8: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#9: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#10: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#11: Chemical ChemComp-MQ7 / MENAQUINONE-7 / Vitamin K2


Mass: 648.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H64O2
#12: Chemical ChemComp-NS5 / 15-cis-1,2-dihydroneurosporene


Mass: 540.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H60
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 6

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Sample preparation

CrystalDensity Matthews: 5 Å3/Da
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.5 Mammonium sulfate1drop
23 Mammonium sulfate1reservoiror 2.6M or 2.4M

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Data collection

DiffractionMean temperature: 263 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.92 / Wavelength: 0.92, 1.0
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1993 / Details: FOCUSING MIRROR, TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
211
ReflectionResolution: 2.4→27.7 Å / Num. obs: 89029 / % possible obs: 79.4 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 6.9
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.287 / % possible all: 60
Reflection
*PLUS
Num. obs: 87694 / Num. measured all: 233535
Reflection shell
*PLUS
% possible obs: 61.1 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4(ROTAVATAdata scaling
Agrovatadata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 2PRC

2prc


Resolution: 2.4→10 Å / Rfactor Rfree error: 0.0023 / Cross valid method: A POSTERIORI / Details: N(OBS)/N(PAR) = 2.07
RfactorNum. reflection% reflectionSelection details
Rfree0.215 8757 10 %RANDOM
Rwork0.178 ---
obs0.178 87694 79.5 %-
Displacement parametersBiso mean: 28.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9342 0 787 425 10554
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.41
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.19
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.4→2.51 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.288 818 10 %
Rwork0.264 7526 -
obs--61.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_TEST.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.IONTOPH19.ION
X-RAY DIFFRACTION3PARHCSDX_IUB.RCVTOPHCSDX_IUB.RCV
X-RAY DIFFRACTION4PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.19
LS refinement shell
*PLUS
Rfactor Rfree: 0.207 / Rfactor obs: 0.168

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