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- PDB-4h13: Crystal Structure of the Cytochrome b6f Complex from Mastigocladu... -

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Basic information

Entry
Database: PDB / ID: 4h13
TitleCrystal Structure of the Cytochrome b6f Complex from Mastigocladus laminosus with TDS
Components
  • (Cytochrome b6-f complex subunit ...) x 5
  • Apocytochrome f
  • Cytochrome b6
  • Cytochrome b6-f complex iron-sulfur subunit
KeywordsPHOTOSYNTHESIS / Alpha helix / beta sheet / Plastoquinol-plastocyanin oxidoreductase / Plastocyanin / Thylakoid membrane
Function / homology
Function and homology information


cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / : / cytochrome complex assembly / photosynthetic electron transport chain / quinol-cytochrome-c reductase activity / plasma membrane-derived thylakoid membrane / : / photosynthesis ...cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / : / cytochrome complex assembly / photosynthetic electron transport chain / quinol-cytochrome-c reductase activity / plasma membrane-derived thylakoid membrane / : / photosynthesis / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / oxidoreductase activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Single helix bin / plastocyanin oxidoreductase / Cytochrome b6-f complex subunit 6 / Cytochrome f large domain / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB ...Single helix bin / plastocyanin oxidoreductase / Cytochrome b6-f complex subunit 6 / Cytochrome f large domain / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily / Cytochrome b6-f complex, subunit 8 superfamily / Cytochrome B6-F complex subunit 5 / PetN / PetM family of cytochrome b6f complex subunit 7 / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / Single helix bin / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / : / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Rieske iron-sulphur protein, C-terminal / Rudiment single hybrid motif / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Up-down Bundle / Beta Barrel / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-7PH / Octadecane / BETA-CAROTENE / : / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / PENTADECANE / N-OCTANE / Chem-OPC ...Chem-7PH / Octadecane / BETA-CAROTENE / : / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / PENTADECANE / N-OCTANE / Chem-OPC / Chem-SQD / Chem-TDS / Cytochrome b6 / Cytochrome b6-f complex subunit 4 / Cytochrome f / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit 8
Similarity search - Component
Biological speciesMastigocladus laminosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsHasan, S.S. / Yamashita, E. / Baniulis, D. / Cramer, W.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Quinone-dependent proton transfer pathways in the photosynthetic cytochrome b6f complex
Authors: Hasan, S.S. / Yamashita, E. / Baniulis, D. / Cramer, W.A.
History
DepositionSep 10, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 2.0Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,21027
Polymers107,6518
Non-polymers9,55819
Water43224
1
A: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules

A: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,41954
Polymers215,30316
Non-polymers19,11638
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area88040 Å2
ΔGint-945 kcal/mol
Surface area77330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.197, 157.197, 363.276
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 3 types, 3 molecules ACD

#1: Protein Cytochrome b6


Mass: 24245.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83791
#3: Protein Apocytochrome f


Mass: 31655.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83793
#4: Protein Cytochrome b6-f complex iron-sulfur subunit / Plastohydroquinone:plastocyanin oxidoreductase iron-sulfur protein / ISP / RISP / Rieske iron-sulfur protein


Mass: 19422.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83794, EC: 1.10.9.1

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Cytochrome b6-f complex subunit ... , 5 types, 5 molecules BEFGH

#2: Protein Cytochrome b6-f complex subunit 4 / 17 kDa polypeptide


Mass: 17687.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83792
#5: Protein/peptide Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex subunit PetL / Cytochrome b6-f complex subunit VI


Mass: 3504.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83795
#6: Protein/peptide Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit PetM / Cytochrome b6-f complex subunit VII


Mass: 3843.595 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83796
#7: Protein/peptide Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit PetG / Cytochrome b6-f complex subunit V


Mass: 4016.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83797
#8: Protein/peptide Cytochrome b6-f complex subunit 8 / Cytochrome b6-f complex subunit PetN / Cytochrome b6-f complex subunit VIII


Mass: 3276.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83798

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Non-polymers , 14 types, 43 molecules

#9: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#10: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#11: Chemical ChemComp-OPC / (7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE / DIOLEOYL-PHOSPHATIDYLCHOLINE


Mass: 801.148 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H87NO8P / Comment: phospholipid*YM
#12: Chemical ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H32
#13: Chemical ChemComp-8K6 / Octadecane / N-Octadecane


Mass: 254.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38
#14: Chemical ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#15: Chemical ChemComp-TDS / 8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE / TRIDECYL-STIGMATELLIN


Mass: 418.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H38O5
#16: Chemical ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#17: Chemical ChemComp-7PH / (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate / PHOSPHATIDIC ACID


Mass: 564.732 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H57O8P
#18: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78O12S
#19: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#20: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#21: Chemical ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56
#22: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHIS RESIDUE WAS PRO ACCORDING TO THE PREVIOUS VERSION OF DATABASE P83793 (CYF_MASLA).

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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: 6.02 Å3/Da / Density % sol: 79.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.07→34.57 Å / Num. all: 50067 / Num. obs: 50067 / Biso Wilson estimate: 91.83 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2E76

2e76


Resolution: 3.07→34.567 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8118 / SU ML: 0.37 / σ(F): 1.35 / Phase error: 25.08 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.238 2544 5.09 %
Rwork0.2136 --
obs0.2148 49966 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 316.07 Å2 / Biso mean: 115.8209 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.03 Å2-0 Å2
2---0.03 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 3.07→34.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7459 0 644 24 8127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058348
X-RAY DIFFRACTIONf_angle_d1.2811378
X-RAY DIFFRACTIONf_dihedral_angle_d20.8413106
X-RAY DIFFRACTIONf_chiral_restr0.1681230
X-RAY DIFFRACTIONf_plane_restr0.0051349
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0682-3.12720.35061140.3062452256694
3.1272-3.1910.37841250.299226302755100
3.191-3.26030.32241340.282425932727100
3.2603-3.33610.28311430.263326212764100
3.3361-3.41940.30291540.25226082762100
3.4194-3.51180.29061410.23525892730100
3.5118-3.6150.23781380.211626202758100
3.615-3.73160.2431420.220626462788100
3.7316-3.86480.2531490.208225872736100
3.8648-4.01930.25011390.204626532792100
4.0193-4.2020.22331320.205926402772100
4.202-4.42310.22171430.191326562799100
4.4231-4.69960.20441530.185126322785100
4.6996-5.06140.23221460.188526762822100
5.0614-5.56880.2151470.20426652812100
5.5688-6.37030.25651410.228527102851100
6.3703-8.00940.20371770.199227272904100
8.0094-34.56880.22381260.21442717284392

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