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- PDB-1q90: Structure of the cytochrome b6f (plastohydroquinone : plastocyani... -

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Basic information

Entry
Database: PDB / ID: 1q90
TitleStructure of the cytochrome b6f (plastohydroquinone : plastocyanin oxidoreductase) from Chlamydomonas reinhardtii
Components
  • (Cytochrome B6-F complex iron-sulfur ...) x 2
  • (Cytochrome b6f complex subunit ...) x 4
  • Apocytochrome f
  • Cytochrome b6
  • Cytochrome b6-f complex subunit 4
KeywordsPHOTOSYNTHESIS / MEMBRANE PROTEIN COMPLEX / ELECTRON TRANSFER / OXYDOREDUCTASE / CHLOROPHYLL / BETA-CAROTENE / STIGMATELLIN / SULFOQUINOVOSYLDIACYLGLYCEROL / MONOGALACTOSYLDIACYLGLYCEROL
Function / homology
Function and homology information


nonphotochemical quenching / cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / : / cytochrome complex assembly / photosynthetic electron transport chain / chloroplast thylakoid membrane / : / photosynthesis ...nonphotochemical quenching / cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / : / cytochrome complex assembly / photosynthetic electron transport chain / chloroplast thylakoid membrane / : / photosynthesis / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial inner membrane / oxidoreductase activity / iron ion binding / mRNA binding / heme binding / metal ion binding / membrane
Similarity search - Function
plastocyanin oxidoreductase / Cytochrome B6-F complex subunit VI (PetL) / Cytochrome b6-f complex subunit 6 / Cytochrome f large domain / 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 ...plastocyanin oxidoreductase / Cytochrome B6-F complex subunit VI (PetL) / Cytochrome b6-f complex subunit 6 / Cytochrome f large domain / 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 / Rieske iron-sulphur protein, C-terminal / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / 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
BETA-CAROTENE / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / HEME C / EICOSANE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-SQD / Chem-TDS / Cytochrome b6-f complex subunit 8, chloroplastic / Cytochrome b6-f complex subunit 4 ...BETA-CAROTENE / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / HEME C / EICOSANE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-SQD / Chem-TDS / Cytochrome b6-f complex subunit 8, chloroplastic / Cytochrome b6-f complex subunit 4 / Cytochrome f / Cytochrome b6-f complex iron-sulfur subunit, chloroplastic / Cytochrome b6-f complex subunit 6 / Cytochrome b6 / Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit 7, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.1 Å
AuthorsStroebel, D. / Choquet, Y. / Popot, J.-L. / Picot, D.
Citation
Journal: Nature / Year: 2003
Title: An Atypical Haem in the Cytochrome B6F Complex
Authors: Stroebel, D. / Choquet, Y. / Popot, J.-L. / Picot, D.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Chimeric Fusions of Subunits IV and PET L in the Cytochrome B6F complex of chlamydomonas reinhardtii: structural implications and consequences on state transitions
Authors: Zito, F. / Vinh, J. / Popot, J.L. / Finazzi, G.
History
DepositionAug 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 25, 2012Group: Non-polymer description
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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_type.id / _struct_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 3.0Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_chiral
Item: _chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE Apocytochrome f (chain A): 6His tag at C-terminus, residues 287-292 Rieske Proteins ...SEQUENCE Apocytochrome f (chain A): 6His tag at C-terminus, residues 287-292 Rieske Proteins (chains C,R): sequence numbering includes signal peptide (residues 1-30). Please see Remark 3 - Other Refinement Remarks Subunit 7 (chain M): sequence numbering includes signal peptide (residues 1-60). PETN subunit (chain N): sequence numbering includes the signal peptide but the beginning of the mature sequence is unknown. Sequence used is that of volvox carteri f. nagariensis according to reference 1.
Remark 600HETEROGEN Ligand SQD: acyl chains unidentified Ligand LFA: putative alkyl chain of lipid Ligand LMG: ...HETEROGEN Ligand SQD: acyl chains unidentified Ligand LFA: putative alkyl chain of lipid Ligand LMG: putative, alkyl chains unidentified

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apocytochrome f
B: Cytochrome b6
C: Cytochrome B6-F complex iron-sulfur subunit
D: Cytochrome b6-f complex subunit 4
R: Cytochrome B6-F complex iron-sulfur subunit
G: Cytochrome b6f complex subunit petG
L: Cytochrome b6f complex subunit petL
M: Cytochrome b6f complex subunit PETM
N: Cytochrome b6f complex subunit PETN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,86321
Polymers106,7129
Non-polymers7,15112
Water362
1
A: Apocytochrome f
B: Cytochrome b6
C: Cytochrome B6-F complex iron-sulfur subunit
D: Cytochrome b6-f complex subunit 4
R: Cytochrome B6-F complex iron-sulfur subunit
G: Cytochrome b6f complex subunit petG
L: Cytochrome b6f complex subunit petL
M: Cytochrome b6f complex subunit PETM
N: Cytochrome b6f complex subunit PETN
hetero molecules

A: Apocytochrome f
B: Cytochrome b6
C: Cytochrome B6-F complex iron-sulfur subunit
D: Cytochrome b6-f complex subunit 4
R: Cytochrome B6-F complex iron-sulfur subunit
G: Cytochrome b6f complex subunit petG
L: Cytochrome b6f complex subunit petL
M: Cytochrome b6f complex subunit PETM
N: Cytochrome b6f complex subunit PETN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,72642
Polymers213,42518
Non-polymers14,30124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
Buried area79110 Å2
ΔGint-824 kcal/mol
Surface area74780 Å2
MethodPISA
2
A: Apocytochrome f
B: Cytochrome b6
C: Cytochrome B6-F complex iron-sulfur subunit
D: Cytochrome b6-f complex subunit 4
R: Cytochrome B6-F complex iron-sulfur subunit
G: Cytochrome b6f complex subunit petG
L: Cytochrome b6f complex subunit petL
M: Cytochrome b6f complex subunit PETM
N: Cytochrome b6f complex subunit PETN
hetero molecules

A: Apocytochrome f
B: Cytochrome b6
C: Cytochrome B6-F complex iron-sulfur subunit
D: Cytochrome b6-f complex subunit 4
R: Cytochrome B6-F complex iron-sulfur subunit
G: Cytochrome b6f complex subunit petG
L: Cytochrome b6f complex subunit petL
M: Cytochrome b6f complex subunit PETM
N: Cytochrome b6f complex subunit PETN
hetero molecules

A: Apocytochrome f
B: Cytochrome b6
C: Cytochrome B6-F complex iron-sulfur subunit
D: Cytochrome b6-f complex subunit 4
R: Cytochrome B6-F complex iron-sulfur subunit
G: Cytochrome b6f complex subunit petG
L: Cytochrome b6f complex subunit petL
M: Cytochrome b6f complex subunit PETM
N: Cytochrome b6f complex subunit PETN
hetero molecules

A: Apocytochrome f
B: Cytochrome b6
C: Cytochrome B6-F complex iron-sulfur subunit
D: Cytochrome b6-f complex subunit 4
R: Cytochrome B6-F complex iron-sulfur subunit
G: Cytochrome b6f complex subunit petG
L: Cytochrome b6f complex subunit petL
M: Cytochrome b6f complex subunit PETM
N: Cytochrome b6f complex subunit PETN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)455,45384
Polymers426,85036
Non-polymers28,60348
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_576x,-y+2,-z+11
Buried area163530 Å2
ΔGint-1680 kcal/mol
Surface area144270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)102.454, 171.205, 351.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe second part of the biological assembly is generated by the two fold axis: -x+1,-y+2,z

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Components

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Protein , 3 types, 3 molecules ABD

#1: Protein Apocytochrome f


Mass: 32109.834 Da / Num. of mol.: 1 / Fragment: Residues 1-292 / Mutation: 6 His tag at C-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Strain: H6F5 / Gene: PETA / Organelle: CHLOROPLAST / Production host: Chlamydomonas reinhardtii (plant) / Strain (production host): H6F5 / References: UniProt: P23577
#2: Protein Cytochrome b6


Mass: 24184.531 Da / Num. of mol.: 1 / Fragment: Residues 4-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Strain: H6F5 / Gene: PETB / Organelle: CHLOROPLAST / Production host: Chlamydomonas reinhardtii (plant) / Strain (production host): H6F5 / References: UniProt: Q00471
#4: Protein Cytochrome b6-f complex subunit 4 / 17 kDa polypeptide


Mass: 17305.580 Da / Num. of mol.: 1 / Fragment: Residues 4-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Strain: H6F5 / Gene: PETD / Organelle: CHLOROPLAST / Production host: Chlamydomonas reinhardtii (plant) / Strain (production host): H6F5 / References: UniProt: Q42496, UniProt: P23230*PLUS

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Cytochrome B6-F complex iron-sulfur ... , 2 types, 2 molecules CR

#3: Protein Cytochrome B6-F complex iron-sulfur subunit / Rieske iron-sulfur protein / RISP


Mass: 13660.400 Da / Num. of mol.: 1 / Fragment: Soluble domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Strain: H6F5 / Gene: PETC / Organelle: CHLOROPLAST / Production host: Chlamydomonas reinhardtii (plant) / Strain (production host): H6F5 / References: UniProt: P49728, EC: 1.10.99.1
#5: Protein/peptide Cytochrome B6-F complex iron-sulfur subunit / Rieske iron-sulfur protein / RISP


Mass: 4707.349 Da / Num. of mol.: 1 / Fragment: Transmembrane domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Strain: H6F5 / Gene: PETC / Organelle: CHLOROPLAST / Production host: Chlamydomonas reinhardtii (plant) / Strain (production host): H6F5
References: UniProt: P23230, UniProt: P49728*PLUS, EC: 1.10.99.1

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Cytochrome b6f complex subunit ... , 4 types, 4 molecules GLMN

#6: Protein/peptide Cytochrome b6f complex subunit petG / Cytochrome b6-f complex subunit V


Mass: 3984.786 Da / Num. of mol.: 1 / Fragment: Residues 1-30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Strain: H6F5 / Gene: PETG / Organelle: CHLOROPLAST / Production host: Chlamydomonas reinhardtii (plant) / Strain (production host): H6F5 / References: UniProt: P49728, UniProt: Q08362*PLUS
#7: Protein/peptide Cytochrome b6f complex subunit petL / Cytochrome b6-f complex subunit VI


Mass: 3438.341 Da / Num. of mol.: 1 / Fragment: Residues 1-32
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Strain: H6F5 / Gene: PETL / Organelle: CHLOROPLAST / Production host: Chlamydomonas reinhardtii (plant) / Strain (production host): H6F5 / References: UniProt: P50369
#8: Protein/peptide Cytochrome b6f complex subunit PETM / Cytochrome b6-f complex subunit 7


Mass: 4037.782 Da / Num. of mol.: 1 / Fragment: Residues 62-95
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Strain: H6F5 / Gene: PETM / Organelle: CHLOROPLAST / Production host: Chlamydomonas reinhardtii (plant) / Strain (production host): H6F5 / References: UniProt: Q08362, UniProt: Q42496*PLUS
#9: Protein/peptide Cytochrome b6f complex subunit PETN


Mass: 3283.840 Da / Num. of mol.: 1 / Fragment: Residues 68-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Strain: H6F5 / Gene: PETN / Organelle: CHLOROPLAST / Production host: Chlamydomonas reinhardtii (plant) / Strain (production host): H6F5 / References: UniProt: P50369, UniProt: P0C1D4*PLUS

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Non-polymers , 9 types, 14 molecules

#10: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#11: Chemical ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56
#12: Chemical ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H42
#13: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#14: Chemical ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#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.: 1 / Source method: obtained synthetically / Formula: C25H38O5
#16: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H86O10
#17: 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
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 7.06 Å3/Da / Density % sol: 82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Reservoir: 25% PEG-MME 350, 40 millimolar TRIS HCL PH 8, 40 millimolar nacl, 0.2 millimolar laurylmaltoside, 30% glycerol. Drop: 1.3 microliter protein + 0.7 microliter reservoir, VAPOR ...Details: Reservoir: 25% PEG-MME 350, 40 millimolar TRIS HCL PH 8, 40 millimolar nacl, 0.2 millimolar laurylmaltoside, 30% glycerol. Drop: 1.3 microliter protein + 0.7 microliter reservoir, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 mMTris-HCl1reservoirpH8
240 mM1reservoirNaCl
30.2 mMDDM1reservoir
430 %(w/v)glycerol1reservoir
525 %(w/v)PEG3501reservoir
610 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.00799 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2002
RadiationMonochromator: Two Si crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00799 Å / Relative weight: 1
ReflectionResolution: 3.1→35 Å / Num. obs: 56687 / % possible obs: 99.6 % / Observed criterion σ(I): 1.8 / Redundancy: 4.6 % / Rsym value: 0.089 / Net I/σ(I): 6.6
Reflection shellResolution: 3.1→3.27 Å / Rsym value: 0.39 / % possible all: 99.6
Reflection
*PLUS
Redundancy: 4.3 % / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 3.1→34.42 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3607425.92 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: In a B6F dimer, a rieske protein is anchored in one monomer by its transmembrane domain (residues 33-71), even though its soluble domain (residues 80-183 and 185-206) lies on the other ...Details: In a B6F dimer, a rieske protein is anchored in one monomer by its transmembrane domain (residues 33-71), even though its soluble domain (residues 80-183 and 185-206) lies on the other monomer. This is why the rieske chain of one monomer is divided into two parts corresponding to two different rieske proteins. The linker (residues 72-79) is not visible. In the soluble domain, the sub-domain corresponding to residues 80-130 and 177-206 is not well defined.
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2848 5.1 %RANDOM
Rwork0.222 ---
obs0.222 56134 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.6136 Å2 / ksol: 0.354968 e/Å3
Displacement parametersBiso mean: 69.9 Å2
Baniso -1Baniso -2Baniso -3
1-8.27 Å20 Å20 Å2
2--18.14 Å20 Å2
3----26.41 Å2
Refine analyzeLuzzati coordinate error free: 0.43 Å / Luzzati sigma a free: 0.53 Å
Refinement stepCycle: LAST / Resolution: 3.1→34.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7330 0 446 2 7778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 460 5 %
Rwork0.314 8740 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2HEC.PARHEC-FREE-PROP.TOP
X-RAY DIFFRACTION3HEM.PARHEM-FREE-PROP.TOP
X-RAY DIFFRACTION4FES.PARFES.TOP
X-RAY DIFFRACTION5CLA.PARCLA.TOP
X-RAY DIFFRACTION6TDS.PARTDS.TOP
X-RAY DIFFRACTION7BCR.PARBCR.TOP
X-RAY DIFFRACTION8SQD.PARSQD.TOP
X-RAY DIFFRACTION9WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION10alk.paralk.top
X-RAY DIFFRACTION11lmg.parlmg.top
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 35 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3
LS refinement shell
*PLUS
Lowest resolution: 3.21 Å / Rfactor Rfree: 0.36 / Rfactor Rwork: 0.34

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