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- PDB-1l9j: X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Ce... -

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Basic information

Entry
Database: PDB / ID: 1l9j
TitleX-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals
Components
  • (REACTION CENTER PROTEIN ...) x 3
  • cytochrome c-2
KeywordsPHOTOSYNTHESIS / bacterial photosynthesis / electron transfer proteins / protein-protein interactions / membrane proteins / protein complexes
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 / membrane => GO:0016020 / photosynthesis / periplasmic space ...: / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / : / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / membrane => GO:0016020 / photosynthesis / periplasmic space / electron transfer activity / heme binding / 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 / Cytochrome c, class IA/ IB / Photosynthetic reaction centre, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit ...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 / Cytochrome c, class IA/ IB / 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 / Cytochrome c / : / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / PROTOPORPHYRIN IX CONTAINING FE / UBIQUINONE-10 / Cytochrome c2 / Reaction center protein M chain / Reaction center protein L chain / Cytochrome c2 / Reaction center protein H chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / : / PROTOPORPHYRIN IX CONTAINING FE / UBIQUINONE-10 / Cytochrome c2 / Reaction center protein M chain / Reaction center protein L chain / Cytochrome c2 / 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: 3.25 Å
AuthorsAxelrod, H.L. / Abresch, E.C. / Okamura, M.Y. / Yeh, A.P. / Rees, D.C. / Feher, G.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: X-ray structure determination of the cytochrome c2: reaction center electron transfer complex from Rhodobacter sphaeroides.
Authors: Axelrod, H.L. / Abresch, E.C. / Okamura, M.Y. / Yeh, A.P. / Rees, D.C. / Feher, G.
History
DepositionMar 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_bond.pdbx_aromatic_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: REACTION CENTER PROTEIN L CHAIN
M: REACTION CENTER PROTEIN M CHAIN
H: REACTION CENTER PROTEIN H CHAIN
C: cytochrome c-2
R: REACTION CENTER PROTEIN L CHAIN
S: REACTION CENTER PROTEIN M CHAIN
T: REACTION CENTER PROTEIN H CHAIN
D: cytochrome c-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,50732
Polymers214,5998
Non-polymers14,90924
Water2,324129
1
L: REACTION CENTER PROTEIN L CHAIN
M: REACTION CENTER PROTEIN M CHAIN
H: REACTION CENTER PROTEIN H CHAIN
C: cytochrome c-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,75416
Polymers107,2994
Non-polymers7,45412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
R: REACTION CENTER PROTEIN L CHAIN
S: REACTION CENTER PROTEIN M CHAIN
T: REACTION CENTER PROTEIN H CHAIN
D: cytochrome c-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,75416
Polymers107,2994
Non-polymers7,45412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.930, 80.312, 246.575
Angle α, β, γ (deg.)90.00, 92.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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REACTION CENTER PROTEIN ... , 3 types, 6 molecules LRMSHT

#1: Protein REACTION CENTER PROTEIN L CHAIN / Photosynthetic reaction center L subunit


Mass: 31346.389 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26 / References: UniProt: P02954, UniProt: P0C0Y8*PLUS
#2: Protein REACTION CENTER PROTEIN M CHAIN / Photosynthetic reaction center M subunit


Mass: 34398.543 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26 / References: UniProt: P02953, UniProt: P0C0Y9*PLUS
#3: Protein REACTION CENTER PROTEIN H CHAIN / Photosynthetic reaction center H subunit


Mass: 28066.322 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26 / References: UniProt: P11846, UniProt: P0C0Y7*PLUS

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Protein , 1 types, 2 molecules CD

#4: Protein cytochrome c-2


Mass: 13488.064 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / Strain: R26 / References: UniProt: P00095, UniProt: P0C0X8*PLUS

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Non-polymers , 8 types, 153 molecules

#5: Chemical
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#6: Chemical
ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H76N4O6
#7: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#10: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#11: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.59 Å3/Da / Density % sol: 65.74 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 4000, lauryl-dimethylamine-N-oxide, heptane-1,2,3-triol, tricine buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 19 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17.7 mg/mlprotein1drop
22 mg/mlcytochrome c21drop
310 %(w/v)PEG40001drop
40.06 %(w/v)LDAO1drop
53.9 %(w/v)heptanetriol1drop
615 mMTricine1droppH8.5
722 %(w/v)PEG40001reservoir
850 mMTricine1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 10, 2000 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: single crystal Si(311) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.25→49.32 Å / Num. all: 47751 / Num. obs: 47751 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 64.3 Å2 / Rsym value: 0.119 / Net I/σ(I): 4.8
Reflection shellResolution: 3.25→3.43 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 6920 / Rsym value: 0.45 / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 348873 / Rmerge(I) obs: 0.119
Reflection shell
*PLUS
% possible obs: 98.8 % / Rmerge(I) obs: 0.45

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID Code 1AIJ and 1CXC are starting models for the reaction center and cytochrome c2 respectively. RESIDUES LISTED IN REMARK 465 ARE MISSING DUE TO LACK OF ELECTRON DENSITY. ATOMS ...Starting model: PDB ID Code 1AIJ and 1CXC are starting models for the reaction center and cytochrome c2 respectively. RESIDUES LISTED IN REMARK 465 ARE MISSING DUE TO LACK OF ELECTRON DENSITY. ATOMS ON THE ISOPRENOID TAIL OF BCL 1001 and 2001, BPH 1005 and 2005, AND U10 1008 and 2008 ARE MISSING DUE TO THE LACK OF ELECTRON DENSITY.

1aij

1cxc


Resolution: 3.25→49.32 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 2385 -random
Rwork0.248 ---
all0.263 47695 --
obs0.263 47695 98.5 %-
Displacement parametersBiso mean: 74.9 Å2
Baniso -1Baniso -2Baniso -3
1-46.477 Å20 Å2-11.191 Å2
2---21.432 Å20 Å2
3----25.045 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 3.25→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14404 0 964 129 15497
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00773
X-RAY DIFFRACTIONc_angle_d1.28
X-RAY DIFFRACTIONc_dihedral_angle_d19.25
X-RAY DIFFRACTIONc_improper_angle_d0.883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
3.25-3.370.3732260.328X-RAY DIFFRACTION473798.4
3.37-3.50.312410.291X-RAY DIFFRACTION474698.5
3.5-3.660.3242550.279X-RAY DIFFRACTION469798.5
3.66-3.850.2862390.243X-RAY DIFFRACTION473598.3
3.85-4.090.322280.24X-RAY DIFFRACTION475698.6
4.09-4.410.2472290.218X-RAY DIFFRACTION473298.4
4.41-4.850.2472570.208X-RAY DIFFRACTION479098.5
4.85-5.560.2892340.236X-RAY DIFFRACTION477798.5
5.56-70.282400.233X-RAY DIFFRACTION480498.5
7-500.282360.262X-RAY DIFFRACTION492198.4
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor all: 0.263 / Rfactor obs: 0.248 / Rfactor Rfree: 0.287 / Rfactor Rwork: 0.248
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.883
LS refinement shell
*PLUS
Rfactor Rfree: 0.373 / Rfactor Rwork: 0.328 / Rfactor obs: 0.328

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