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- PDB-1p84: HDBT inhibited Yeast Cytochrome bc1 Complex -

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Basic information

Entry
Database: PDB / ID: 1p84
TitleHDBT inhibited Yeast Cytochrome bc1 Complex
Components
  • (Ubiquinol-cytochrome C reductase complex ...) x 6
  • Cytochrome c1, heme protein
  • Heavy Chain (Vh) Of Fv-Fragment
  • Light Chain (Vl) Of Fv-Fragment
  • Ubiquinol-cytochrome C reductase iron-sulfur subunit
  • cytochrome b
KeywordsOXIDOREDUCTASE / cytochrome bc1 complex / complex III / ubiquinol / cytochrome c oxidoreductase / hydroxyquinone / HHDBT / Qo site / phospholipid / membrane protein
Function / homology
Function and homology information


matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / cellular respiration / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista ...matrix side of mitochondrial inner membrane / protein processing involved in protein targeting to mitochondrion / Respiratory electron transport / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / cellular respiration / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / aerobic respiration / proton transmembrane transport / nuclear periphery / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / metal ion binding / cytosol
Similarity search - Function
Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain A, domain 1 ...Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / 3-layer Sandwich / Cytochrome b / : / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / 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 / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / CARDIOLIPIN / 5-HEPTYL-6-HYDROXY-1,3-BENZOTHIAZOLE-4,7-DIONE / FE2/S2 (INORGANIC) CLUSTER / HEME C / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Chem-UQ6 / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7, mitochondrial ...1,2-Distearoyl-sn-glycerophosphoethanolamine / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / CARDIOLIPIN / 5-HEPTYL-6-HYDROXY-1,3-BENZOTHIAZOLE-4,7-DIONE / FE2/S2 (INORGANIC) CLUSTER / HEME C / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Chem-UQ6 / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7, mitochondrial / Cytochrome b / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 8, mitochondrial / Cytochrome b-c1 complex subunit 9, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Positional, B-factor refinement / Resolution: 2.5 Å
AuthorsPalsdottir, H. / Lojero, C.G. / Trumpower, B.L. / Hunte, C.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure of the yeast cytochrome bc1 complex with a hydroxyquinone anion Qo site inhibitor bound
Authors: Palsdottir, H. / Lojero, C.G. / Trumpower, B.L. / Hunte, C.
History
DepositionMay 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2017Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_residues
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 2.0Mar 3, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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 2.1Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquinol-cytochrome C reductase complex core protein I
B: Ubiquinol-cytochrome C reductase complex core protein 2
C: cytochrome b
D: Cytochrome c1, heme protein
E: Ubiquinol-cytochrome C reductase iron-sulfur subunit
F: Ubiquinol-cytochrome C reductase complex 17 kDa protein
G: Ubiquinol-cytochrome C reductase complex 14 kDa protein
H: Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C
I: Ubiquinol-cytochrome C reductase complex 7.3 kDa protein
J: Heavy Chain (Vh) Of Fv-Fragment
K: Light Chain (Vl) Of Fv-Fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,73624
Polymers244,17611
Non-polymers8,56013
Water5,873326
1
A: Ubiquinol-cytochrome C reductase complex core protein I
B: Ubiquinol-cytochrome C reductase complex core protein 2
C: cytochrome b
D: Cytochrome c1, heme protein
E: Ubiquinol-cytochrome C reductase iron-sulfur subunit
F: Ubiquinol-cytochrome C reductase complex 17 kDa protein
G: Ubiquinol-cytochrome C reductase complex 14 kDa protein
H: Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C
I: Ubiquinol-cytochrome C reductase complex 7.3 kDa protein
hetero molecules

A: Ubiquinol-cytochrome C reductase complex core protein I
B: Ubiquinol-cytochrome C reductase complex core protein 2
C: cytochrome b
D: Cytochrome c1, heme protein
E: Ubiquinol-cytochrome C reductase iron-sulfur subunit
F: Ubiquinol-cytochrome C reductase complex 17 kDa protein
G: Ubiquinol-cytochrome C reductase complex 14 kDa protein
H: Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C
I: Ubiquinol-cytochrome C reductase complex 7.3 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)452,88844
Polymers435,76718
Non-polymers17,12126
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area105220 Å2
ΔGint-860 kcal/mol
Surface area154400 Å2
MethodPISA
2
J: Heavy Chain (Vh) Of Fv-Fragment
K: Light Chain (Vl) Of Fv-Fragment


  • defined by author&software
  • 26.3 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)26,2922
Polymers26,2922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-15 kcal/mol
Surface area11120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.998, 165.091, 147.525
Angle α, β, γ (deg.)90.00, 117.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Ubiquinol-cytochrome C reductase complex ... , 6 types, 6 molecules ABFGHI

#1: Protein Ubiquinol-cytochrome C reductase complex core protein I


Mass: 47445.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P07256, quinol-cytochrome-c reductase
#2: Protein Ubiquinol-cytochrome C reductase complex core protein 2


Mass: 38751.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P07257, quinol-cytochrome-c reductase
#6: Protein Ubiquinol-cytochrome C reductase complex 17 kDa protein / Mitochondrial hinge protein / Complex III polypeptide VI


Mass: 8854.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P00127, quinol-cytochrome-c reductase
#7: Protein Ubiquinol-cytochrome C reductase complex 14 kDa protein


Mass: 14355.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P00128, quinol-cytochrome-c reductase
#8: Protein Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C


Mass: 10856.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P08525, quinol-cytochrome-c reductase
#9: Protein Ubiquinol-cytochrome C reductase complex 7.3 kDa protein


Mass: 6301.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P22289, quinol-cytochrome-c reductase

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Protein , 3 types, 3 molecules CDE

#3: Protein cytochrome b /


Mass: 43674.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P00163, quinol-cytochrome-c reductase
#4: Protein Cytochrome c1, heme protein /


Mass: 27521.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P07143, quinol-cytochrome-c reductase
#5: Protein Ubiquinol-cytochrome C reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP


Mass: 20122.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Organelle: MITOCHONDRIAMitochondrion / References: UniProt: P08067, quinol-cytochrome-c reductase

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Antibody , 2 types, 2 molecules JK

#10: Antibody Heavy Chain (Vh) Of Fv-Fragment


Mass: 14365.817 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pASK68 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83
#11: Antibody Light Chain (Vl) Of Fv-Fragment


Mass: 11926.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pASK68 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83

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Non-polymers , 10 types, 339 molecules

#12: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID / Phosphatidic acid


Mass: 704.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H77O8P
#13: Chemical ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#14: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#15: Chemical ChemComp-DBT / 5-HEPTYL-6-HYDROXY-1,3-BENZOTHIAZOLE-4,7-DIONE


Mass: 279.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17NO3S
#16: Chemical ChemComp-UQ6 / 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22-HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE-1,4-DIOL


Mass: 592.891 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H60O4
#17: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Phosphatidylethanolamine


Mass: 748.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#18: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#19: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#20: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#21: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 7

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Sample preparation

CrystalDensity Matthews: 4.76 Å3/Da / Density % sol: 74.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mg/mlprotein1drop
25 %PEG40001reservoirpH7.5
30.05 %n-undecyl-beta-D-maltopyranoside1reservoir
410000 nMHHDBT1reservoirpH8.0
5Tris-HCl1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 4, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 149103 / % possible obs: 92.4 % / Redundancy: 2.5 % / Biso Wilson estimate: 50.3 Å2 / Limit h max: 76 / Limit h min: -86 / Limit k max: 66 / Limit k min: -86 / Limit l max: 59 / Limit l min: 0 / Observed criterion F max: 315600.93 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.4
Reflection shellResolution: 2.5→2.56 Å / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 1.2 / Num. unique all: 9128 / % possible all: 84.6
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 372220
Reflection shell
*PLUS
% possible obs: 84.6 % / Num. unique obs: 9128 / Num. measured obs: 19194 / Rmerge(I) obs: 0.373

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: Positional, B-factor refinement
Starting model: pdb entry 1KB9, protein only

1kb9


Resolution: 2.5→25 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 3677 2.5 %RANDOM
Rwork0.228 ---
obs-145617 92.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 31.4444 Å2 / ksol: 0.245901 e/Å3
Displacement parametersBiso max: 173.4 Å2 / Biso mean: 71.95 Å2 / Biso min: 19.77 Å2
Refine analyzeLuzzati d res high obs: 2.5
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17235 0 508 326 18069
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_torsion_deg23.2
X-RAY DIFFRACTIONc_torsion_impr_deg1.21
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.5-2.520.411672.20.4125080.053110257582.8
2.52-2.530.41812.60.4125640.0463141264584.2
2.53-2.550.404601.90.40326370.0523217269783.8
2.55-2.570.386571.80.38626360.0513188269384.5
2.57-2.590.383501.60.38326300.0543170268084.5
2.59-2.610.36682.20.36126620.0443161273086.3
2.61-2.630.353682.10.35326690.0433182273786
2.63-2.650.37832.60.37126420.0413179272585.7
2.65-2.670.358782.40.35927030.0413201278186.9
2.67-2.690.346320.3426410.0433110270486.9
2.69-2.720.336672.10.33727540.0413235282187.2
2.72-2.740.324712.30.32526820.0383140275387.6
2.74-2.760.317822.60.31927550.0353201283788.6
2.76-2.790.311702.20.31227250.0373145279588.9
2.79-2.820.313702.20.31427960.0373161286690.7
2.82-2.840.3722.30.30127800.0353169285290
2.84-2.870.297792.50.29827540.0333152283389.9
2.87-2.90.284732.30.28628000.0333180287390.3
2.9-2.930.29581.90.29227950.0383116285391.5
2.93-2.960.286420.28128940.0353211295892.1
2.96-30.27722.30.27128450.0323142291792.8
3-3.030.278792.50.27928740.0313190295392.6
3.03-3.070.267872.70.26828500.0293178293792.4
3.07-3.110.251732.30.25328460.0293114291993.7
3.11-3.150.255692.20.25629230.0313198299293.5
3.15-3.190.253712.30.25428420.033111291393.6
3.19-3.240.2536420.25429230.0323161298794.5
3.24-3.290.243802.50.24329320.0273174301294.9
3.29-3.340.228682.20.22829120.0283159298094.3
3.34-3.390.2266420.22629450.0283156300995.3
3.39-3.450.225782.50.22429270.0253153300595.3
3.45-3.510.224792.50.22329530.0253178303295.4
3.51-3.580.223832.60.22329370.0253154302095.8
3.58-3.650.21822.60.2129520.0233166303495.8
3.65-3.730.203782.50.20229100.0233127298895.6
3.73-3.820.202862.70.20129510.0223160303796.1
3.82-3.910.198862.70.19729560.0213165304296.1
3.91-4.020.192652.10.19129920.0243164305796.6
4.02-4.140.191983.10.1929290.0193135302796.5
4.14-4.270.195792.50.19429820.0223162306196.8
4.27-4.420.197742.30.19629920.0233162306697
4.42-4.60.185832.60.18329610.023165304496.2
4.6-4.80.186712.20.18529620.0223167303395.8
4.8-5.060.204732.30.20429840.0243161305796.7
5.06-5.370.199862.70.229630.0213157304996.6
5.37-5.780.2126420.21429930.0263157305796.8
5.78-6.350.206772.40.20830440.0243202312197.5
6.35-7.250.203842.60.20529800.0223171306496.6
7.25-9.060.162752.30.16129550.0193193303094.9
9.06-24.580.203682.10.20126980.0253234276685.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2water.1.paramwater_mod.1.top
X-RAY DIFFRACTION3070303parhcsdx_iub.+lip_trun.bc1070303tophcsdx_iub.+lip_trun.bc1
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.298
LS refinement shell
*PLUS
Rfactor Rwork: 0.41

+
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