[English] 日本語
Yorodumi
- PDB-3l73: Cytochrome BC1 complex from chicken with triazolone inhibitor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3l73
TitleCytochrome BC1 complex from chicken with triazolone inhibitor
Components
  • (CYTOCHROME B-C1 COMPLEX SUBUNIT ...) x 2
  • (MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE ...) x 4
  • (MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN ...) x 2
  • CYTOCHROME B
  • MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN
KeywordsOXIDOREDUCTASE / CYTOCHROME BC1 / MEMBRANE PROTEIN / HEME PROTEIN / RIESKE IRON SULFUR PROTEIN / CYTOCHROME B / CYTOCHROME C1 / COMPLEX III / MITOCHONDRIAL PROCESSING PROTEIN / UBIQUINONE / AZOXYSTROBIN OXIDOREDUCTASE / REDOX ENZYME RESPIRATORY CHAIN / ELECTRON TRANSPORT / HEME / INNER MEMBRANE / MEMBRANE / STROBILURINS BINDING / MITOCHONDRION / TRANSMEMBRANE / STIGMATELLIN / IRON / MITOCHONDRIAL INNER MEMBRANE / RESPIRATORY CHAIN / IRON-SULFUR / TRANSIT PEPTIDE / Metal-binding / Mitochondrion inner membrane / Transport / Disulfide bond
Function / homology
Function and homology information


Respiratory electron transport / quinol-cytochrome-c reductase / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane ...Respiratory electron transport / quinol-cytochrome-c reductase / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / response to oxidative stress / oxidoreductase activity / heme binding / mitochondrion / metal ion binding / cytoplasm
Similarity search - Function
Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain I / 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 Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain I / 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 / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / 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. / 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 / Ribbon / Helix Hairpins / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-JZZ / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer / Mitochondrial cytochrome c1, heme protein / Complex III subunit 9 / Cytochrome b-c1 complex subunit 6 ...CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-JZZ / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer / Mitochondrial cytochrome c1, heme protein / Complex III subunit 9 / Cytochrome b-c1 complex subunit 6 / Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2 / Cytochrome b-c1 complex subunit 7 / Mitochondrial ubiquinol-cytochrome-c reductase complex core protein i / Cytochrome b-c1 complex subunit 8 / Cytochrome b / Cytochrome b-c1 complex subunit Rieske, mitochondrial
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 3.04 Å
AuthorsHuang, L. / Berry, E.A.
CitationJournal: To be Published
Title: Famoxadone and related inhibitors bind like methoxy acrylate inhibitors in the Qo site of the BC1 compl and fix the rieske iron-sulfur protein in a positio close to but distinct from that seen ...Title: Famoxadone and related inhibitors bind like methoxy acrylate inhibitors in the Qo site of the BC1 compl and fix the rieske iron-sulfur protein in a positio close to but distinct from that seen with stigmatellin and other "DISTAL" Qo inhibitors.
Authors: Huang, L. / Berry, E.A.
History
DepositionDec 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 29, 2014Group: Non-polymer description
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Sep 6, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
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.label_atom_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I
B: MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2
C: CYTOCHROME B
D: MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN
E: CYTOCHROME B-C1 COMPLEX SUBUNIT 5, RIESKE IRONSULFUR PROTEIN, MITOCHONDRIAL
F: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN
G: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C
H: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII
I: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
J: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN
N: MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I
O: MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2
P: CYTOCHROME B
Q: MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN
R: CYTOCHROME B-C1 COMPLEX SUBUNIT 5, RIESKE IRONSULFUR PROTEIN, MITOCHONDRIAL
S: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN
T: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C
U: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII
V: CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL
W: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)480,48349
Polymers462,06520
Non-polymers18,41829
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area101720 Å2
ΔGint-689 kcal/mol
Surface area156520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.499, 182.934, 241.028
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsThe deposited coordinates (20 chains plus hetero groups) make up the asymmetric unit which is the biological assembly. One other subunit of the biological assembly (Subunit 11) is lost during purification or crystallization and is not present in the deposited structure.

-
Components

-
MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN ... , 2 types, 4 molecules ANBO

#1: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I


Mass: 49503.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: D0VX31, quinol-cytochrome-c reductase
#2: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2


Mass: 46683.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: D0VX29, quinol-cytochrome-c reductase

-
Protein , 2 types, 4 molecules CPDQ

#3: Protein CYTOCHROME B / / UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CYTOCHROME B SUBUNIT / CYTOCHROME B-C1 COMPLEX SUBUNIT 3 / ...UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CYTOCHROME B SUBUNIT / CYTOCHROME B-C1 COMPLEX SUBUNIT 3 / COMPLEX III SUBUNIT 3 / COMPLEX III SUBUNIT III


Mass: 42622.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: P18946, quinol-cytochrome-c reductase
#4: Protein MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN


Mass: 26973.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: D0VX26, quinol-cytochrome-c reductase

-
CYTOCHROME B-C1 COMPLEX SUBUNIT ... , 2 types, 4 molecules ERIV

#5: Protein CYTOCHROME B-C1 COMPLEX SUBUNIT 5, RIESKE IRONSULFUR PROTEIN, MITOCHONDRIAL / UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT / RIESKE IRON-SULFUR PROTEIN / RISP / COMPLEX ...UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT / RIESKE IRON-SULFUR PROTEIN / RISP / COMPLEX III SUBUNIT 5


Mass: 21506.188 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 77-272 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: Q5ZLR5, quinol-cytochrome-c reductase
#9: Protein/peptide CYTOCHROME B-C1 COMPLEX SUBUNIT RIESKE, MITOCHONDRIAL / UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT / RIESKE IRON-SULFUR PROTEIN / RISP / COMPLEX ...UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT / RIESKE IRON-SULFUR PROTEIN / RISP / COMPLEX III SUBUNIT 5


Mass: 4785.649 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 45-76 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: Q5ZLR5, quinol-cytochrome-c reductase

-
MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE ... , 4 types, 8 molecules FSGTHUJW

#6: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN


Mass: 13394.397 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: D0VX30, quinol-cytochrome-c reductase
#7: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C


Mass: 9498.735 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: D0VX32, quinol-cytochrome-c reductase
#8: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII


Mass: 9057.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: D0VX28, quinol-cytochrome-c reductase
#10: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN


Mass: 7005.963 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GALLUS GALLUS (chicken) / References: UniProt: D0VX27, quinol-cytochrome-c reductase

-
Sugars , 1 types, 5 molecules

#18: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 9 types, 43 molecules

#11: Chemical
ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / Discrete optimized protein energy


Mass: 744.034 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#12: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#13: Chemical ChemComp-JZZ / 4-[7-(3,3-dimethylbut-1-yn-1-yl)naphthalen-1-yl]-5-methoxy-2-methyl-2,4-dihydro-3H-1,2,4-triazol-3-one


Mass: 335.400 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H21N3O2
#14: Chemical ChemComp-UQ / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#15: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#16: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#17: 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.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#19: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#20: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE COMPLETE SEQUENCE OF CHAIN I AND V IS ...THE COMPLETE SEQUENCE OF CHAIN I AND V IS MLSVAARSGPFAPYLSAAAHAVPGPLKALAPAALRAEKVVLDLKRPLLCRESMSGRSARRDLVAGISLNAPASVRY, UNP residues 1-76. THE N-TERMINUS IS DISORDERED.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.02 Å3/Da / Density % sol: 69.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.77
Details: FINAL CONCENTRATIONS BEFORE DIFFUSION: 50 MM CACODYLATE, 9.4 MM TRISHCL, 10 MM MGCL2, 50 G/L GLYCEROL, 30 G/L PEG 3350DA, 0.23 MM EDTA, 0.47 G/L UNDECYL MALTOSIDE, 31 MM OCTYL GLUCOSIDE, PH ...Details: FINAL CONCENTRATIONS BEFORE DIFFUSION: 50 MM CACODYLATE, 9.4 MM TRISHCL, 10 MM MGCL2, 50 G/L GLYCEROL, 30 G/L PEG 3350DA, 0.23 MM EDTA, 0.47 G/L UNDECYL MALTOSIDE, 31 MM OCTYL GLUCOSIDE, PH 6.77, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 26, 2006
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.9→25 Å / Num. all: 167200 / Num. obs: 167200 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 80.8 Å2 / Rsym value: 0.085 / Net I/σ(I): 19.38
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.072 / Num. unique all: 8264 / % possible all: 99.7

-
Processing

Software
NameClassification
Blu-Icedata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: RIGID BODY REFINEMENT
Starting model: PDB ENTRY 3H1H

3h1h


Resolution: 3.04→24.97 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3513358.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 2854 2 %RANDOM
Rwork0.259 ---
all0.2597 145117 --
obs0.2597 145117 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 21.5201 Å2 / ksol: 0.241878 e/Å3
Displacement parametersBiso mean: 86.5 Å2
Baniso -1Baniso -2Baniso -3
1-42 Å20 Å20 Å2
2---22.51 Å20 Å2
3----19.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.94 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 3.04→24.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31794 0 832 19 32645
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it1.662
X-RAY DIFFRACTIONc_scangle_it2.732.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.04→3.2 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.422 384 1.9 %
Rwork0.385 20157 -
obs-20157 99.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2hetero10.par&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3prr.par&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4water.param&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5prosth3.par&_1_TOPOLOGY_INFILE_5

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more