[English] 日本語
Yorodumi
- PDB-4u3f: Cytochrome bc1 complex from chicken with designed inhibitor bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4u3f
TitleCytochrome bc1 complex from chicken with designed inhibitor bound
Components
  • (Cytochrome b-c1 complex subunit ...) x 4
  • (Mitochondrial ubiquinol-cytochrome c reductase ...) x 2
  • (Mitochondrial ubiquinol-cytochrome-c reductase complex core protein ...) x 2
  • Cytochrome b
  • Mitochondrial cytochrome c1, heme protein
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / CYTOCHROME BC1 / MEMBRANE PROTEIN / HEME PROTEIN / RIESKE IRON SULFUR PROTEIN / CYTOCHROME B / CYTOCHROME C1 / UBIQUINONE / COMPLEX III / STROBILURINS / AZOXYSTROBIN / STIGMATELLIN / OXIDOREDUCTASE / REDOX ENZYME RESPIRATORY CHAIN / ELECTRON TRANSPORT / HEME / INNER MEMBRANE / MEMBRANE BINDING / MITOCHONDRION / TRANSMEMBRANE / IRON / MITOCHONDRIAL INNER MEMBRANE / RESPIRATORY CHAIN / 2FE-2S / IRON-SULFUR / METAL-BINDING / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Respiratory electron transport / quinol-cytochrome-c reductase / mitochondrial processing peptidase complex / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c ...Respiratory electron transport / quinol-cytochrome-c reductase / mitochondrial processing peptidase complex / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / aerobic respiration / catalytic activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / response to oxidative stress / membrane => GO:0016020 / oxidoreductase activity / ubiquitin protein ligase binding / heme binding / mitochondrion / nucleoplasm / metal ion binding / cytosol / 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 / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / UBIQUINONE-10 / Chem-Y52 / 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 / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / UBIQUINONE-10 / Chem-Y52 / 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 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Cytochrome b / Cytochrome b-c1 complex subunit Rieske, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2312 Å
AuthorsHuang, L.-S. / Zhu, X.-L. / Yang, G.F. / Berry, E.A.
CitationJournal: Sci Rep / Year: 2015
Title: Rational Design of Highly Potent and Slow-Binding Cytochrome bc1 Inhibitor as Fungicide by Computational Substitution Optimization
Authors: Hao, G.-F. / Yang, S.-G. / Huang, W. / Wang, L. / Shen, Y.-Q. / Tu, W.-L. / Li, H. / Huang, L.-S. / Wu, J.-W. / Berry, E.A. / Yang, G.-F.
History
DepositionJul 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Sep 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_poly / 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 / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code_can / _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 Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-c
H: Cytochrome b-c1 complex subunit 6
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 Rieske, mitochondrial
S: Cytochrome b-c1 complex subunit 7
T: Mitochondrial ubiquinol-cytochrome c reductase ubiquinone-binding protein qp-c
U: Cytochrome b-c1 complex subunit 6
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)492,10556
Polymers467,99220
Non-polymers24,11336
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area108430 Å2
ΔGint-753 kcal/mol
Surface area153400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.251, 181.483, 239.631
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27
18
28
19
29
110
210
111
211
112
212
113
213
114
214
115
215
116
216
117
217

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (RESID 11:215 and not (resid 17:22 or...
211chain N and (RESID 11:215 and not (resid 17:22 or...
112chain A and (RESID 220:225)
212chain N and (RESID 220:225)
113chain A and (RESID 227:443 and not (resid 344 ))
213chain N and (RESID 227:443 and not (resid 344 ))
114chain B and (RESID 24:211 and not (resid 28:31 or resid 189))
214chain O and (RESID 24:211 and not (resid 28:31 or resid 189))
115chain B and (RESID 212:220)
215chain O and (RESID 212:220)
116chain B and (RESID 228:230)
216chain O and (RESID 228:230)
117chain B and (RESID 231:259) and not (resid 236)
217chain O and (RESID 231:259) and not (resid 236)
118chain B and (RESID 271:439) and not resid 392
218chain O and (RESID 271:439) and not resid 392
119chain C and (RESID 3:23 ) and not resid 13
219chain P and (RESID 3:23 ) and not resid 13
1110chain C and (RESID 24:502 and not (resid 240 or resid 270 or resid 154:160))
2110chain P and (RESID 24:502 and not (resid 240 or resid 270 or resid 154:160))
1111chain D and not (resid 1:2 or resid 240:241 or resid 76 or resid 170)
2111chain Q and not (resid 1:2 or resid 240:241 or resid 76 or resid 170)
1112chain E and (RESID 1:65 )
2112chain R and (RESID 1:65 )
1113chain E and (RESID 66:69 )
2113chain R and (RESID 66:69 )
1114chain E and (RESID 153:168 or resid 501 ) and not resid 157
2114chain R and (RESID 153:168 or resid 501 ) and not resid 157
1115(chain F and (RESID 16:108) and not (resid 17 or resid 87 or resid 95 or resid 99))
2115(chain S and (RESID 16:108) and not (resid 17 or resid 87 or resid 95 or resid 99))
1116(chain g and (RESID 3:76) and not (resid 24))
2116(chain t and (RESID 3:76) and not (resid 24))
1117(chain I and (RESID 70:73))
2117(chain V and (RESID 70:73))

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17

-
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) / Tissue: heart
References: UniProt: D0VX31, UniProt: F1NAC6*PLUS, 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, UniProt: F1P582*PLUS, quinol-cytochrome-c reductase

-
Protein , 2 types, 4 molecules CPDQ

#3: Protein Cytochrome b / / Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol- ...Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


Mass: 42650.984 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P18946
#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 ... , 4 types, 8 molecules ERFSHUIV

#5: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron- ...Complex III subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron-sulfur subunit


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
#6: Protein Cytochrome b-c1 complex subunit 7


Mass: 13394.397 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX30
#8: Protein Cytochrome b-c1 complex subunit 6 / Complex III subunit 6 / Mitochondrial hinge protein


Mass: 9057.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX28
#9: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron- ...Complex III subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 7721.136 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 ... , 2 types, 4 molecules GTJW

#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
#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, UniProt: F1NC51*PLUS, quinol-cytochrome-c reductase

-
Sugars , 1 types, 3 molecules

#19: 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.: 3 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 10 types, 44 molecules

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


Mass: 744.034 Da / Num. of mol.: 14 / 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-Y52 / methyl (2E)-3-methoxy-2-(2-{[(5-methoxy-1,3-benzothiazol-2-yl)sulfanyl]methyl}phenyl)prop-2-enoate


Mass: 401.499 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19NO4S2
#14: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#15: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#16: 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
#17: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#18: 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
#20: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


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


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsThe authors do not know the registration of a region of the sequence in chains I and V and are ...The authors do not know the registration of a region of the sequence in chains I and V and are represented by UNK residues

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.35 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6.77
Details: CRYSTALLIZATION CONDITIONS: 50 MM CACODYLATE, 9.4 MM TRISHCL, 30 MM K-MES, 1.8 MM K-MOPS, 30 MM NACL, 31 MM KCL, 10 MM MGCL2, 91 G/L GLYCEROL, 30 G/L PEG 4KDA, 0.9 MM NAN3, 0.05 MM EDTA, 0. ...Details: CRYSTALLIZATION CONDITIONS: 50 MM CACODYLATE, 9.4 MM TRISHCL, 30 MM K-MES, 1.8 MM K-MOPS, 30 MM NACL, 31 MM KCL, 10 MM MGCL2, 91 G/L GLYCEROL, 30 G/L PEG 4KDA, 0.9 MM NAN3, 0.05 MM EDTA, 0.47G/L UNDECYL MALTOSIDE, 31 MM OCTYL GLUCOSIDE, PH 6.77, TEMPERATURE 278K
PH range: 6.77

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9181 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 19, 2011 / Details: capillary microfocus
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9181 Å / Relative weight: 1
ReflectionResolution: 3.23→15 Å / Num. obs: 115416 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rsym value: 0.301 / Net I/σ(I): 6.49
Reflection shellResolution: 3.23→3.29 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.14 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1745)refinement
O12model building
PHENIXmodel building
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TGU

3tgu


Resolution: 3.2312→14.996 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2836 2260 1.98 %random
Rwork0.2364 ---
obs0.2374 113869 98.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2312→14.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31753 0 1016 11 32780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00333593
X-RAY DIFFRACTIONf_angle_d0.68245537
X-RAY DIFFRACTIONf_dihedral_angle_d15.47412326
X-RAY DIFFRACTIONf_chiral_restr0.0264946
X-RAY DIFFRACTIONf_plane_restr0.0045770
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1482X-RAY DIFFRACTIONPOSITIONAL
12N1482X-RAY DIFFRACTIONPOSITIONAL0.004
21A54X-RAY DIFFRACTIONPOSITIONAL
22N54X-RAY DIFFRACTIONPOSITIONAL0.014
31A1680X-RAY DIFFRACTIONPOSITIONAL
32N1680X-RAY DIFFRACTIONPOSITIONAL0.005
41B1405X-RAY DIFFRACTIONPOSITIONAL
42O1405X-RAY DIFFRACTIONPOSITIONAL0.005
51B71X-RAY DIFFRACTIONPOSITIONAL
52O71X-RAY DIFFRACTIONPOSITIONAL0.008
61B15X-RAY DIFFRACTIONPOSITIONAL
62O15X-RAY DIFFRACTIONPOSITIONAL0.007
71B204X-RAY DIFFRACTIONPOSITIONAL
72O204X-RAY DIFFRACTIONPOSITIONAL0.005
81B1218X-RAY DIFFRACTIONPOSITIONAL
82O1218X-RAY DIFFRACTIONPOSITIONAL0.003
91C159X-RAY DIFFRACTIONPOSITIONAL
92P159X-RAY DIFFRACTIONPOSITIONAL0.007
101C2839X-RAY DIFFRACTIONPOSITIONAL
102P2839X-RAY DIFFRACTIONPOSITIONAL0.004
111D1893X-RAY DIFFRACTIONPOSITIONAL
112Q1893X-RAY DIFFRACTIONPOSITIONAL0.005
121E488X-RAY DIFFRACTIONPOSITIONAL
122R488X-RAY DIFFRACTIONPOSITIONAL0.004
131E28X-RAY DIFFRACTIONPOSITIONAL
132R28X-RAY DIFFRACTIONPOSITIONAL0.005
141E115X-RAY DIFFRACTIONPOSITIONAL
142R115X-RAY DIFFRACTIONPOSITIONAL0.008
151F782X-RAY DIFFRACTIONPOSITIONAL
152S782X-RAY DIFFRACTIONPOSITIONAL0.005
161G606X-RAY DIFFRACTIONPOSITIONAL
162T606X-RAY DIFFRACTIONPOSITIONAL0.007
171I28X-RAY DIFFRACTIONPOSITIONAL
172V28X-RAY DIFFRACTIONPOSITIONAL0.007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2312-3.30070.3691260.33075412X-RAY DIFFRACTION77
3.3007-3.37660.36221660.3116975X-RAY DIFFRACTION99
3.3766-3.46010.31461480.30286984X-RAY DIFFRACTION100
3.4601-3.55240.34531380.27617019X-RAY DIFFRACTION100
3.5524-3.65550.32041340.26797052X-RAY DIFFRACTION100
3.6555-3.77170.30371480.26527005X-RAY DIFFRACTION100
3.7717-3.90420.31931590.25697034X-RAY DIFFRACTION100
3.9042-4.05760.31191360.2587055X-RAY DIFFRACTION100
4.0576-4.23820.2961610.25827003X-RAY DIFFRACTION99
4.2382-4.45610.32151240.23697063X-RAY DIFFRACTION100
4.4561-4.72710.28531540.22937041X-RAY DIFFRACTION99
4.7271-5.07890.25811300.21347129X-RAY DIFFRACTION100
5.0789-5.56610.23551440.21697110X-RAY DIFFRACTION100
5.5661-6.31820.25971200.22527154X-RAY DIFFRACTION100
6.3182-7.77130.22331320.19887221X-RAY DIFFRACTION100
7.7713-14.99620.1971400.15557352X-RAY DIFFRACTION100

+
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