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- PDB-1sqx: Crystal Structure Analysis of Bovine Bc1 with Stigmatellin A -

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Basic information

Entry
Database: PDB / ID: 1sqx
TitleCrystal Structure Analysis of Bovine Bc1 with Stigmatellin A
Components
  • (Ubiquinol-cytochrome C reductase complex ...) x 5
  • (Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...) x 2
  • (Ubiquinol-cytochrome-c reductase complex core protein ...) x 2
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
KeywordsOXIDOREDUCTASE / cytochrome bc1 / Qo inhibitor / membrane protein / electron transport
Function / homology
Function and homology information


mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / ubiquinone binding / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain ...mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / ubiquinone binding / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / membrane / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / 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 b-c1 complex subunit 10 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / 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 b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / 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 / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / 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
FE2/S2 (INORGANIC) CLUSTER / HEME C / STIGMATELLIN A / UBIQUINONE-2 / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 9 / Cytochrome b / Cytochrome b-c1 complex subunit 10 ...FE2/S2 (INORGANIC) CLUSTER / HEME C / STIGMATELLIN A / UBIQUINONE-2 / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 9 / Cytochrome b / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsEsser, L. / Quinn, B. / Li, Y.F. / Zhang, M. / Elberry, M. / Yu, L. / Yu, C.A. / Xia, D.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystallographic studies of quinol oxidation site inhibitors: a modified classification of inhibitors for the cytochrome bc(1) complex.
Authors: Esser, L. / Quinn, B. / Li, Y.F. / Zhang, M. / Elberry, M. / Yu, L. / Yu, C.A. / Xia, D.
#1: Journal: Science / Year: 1997
Title: Crystal structure of the cytochrome bc1 complex from bovine heart mitochondria.
Authors: Xia, D. / Yu, C.A. / Kim, H. / Xia, J.Z. / Kachurin, A.M. / Zhang, L. / Yu, L. / Deisenhofer, J.
#2: Journal: Biochemistry / Year: 2002
Title: The crystal structure of mitochondrial cytochrome bc1 in complex with famoxadone: the role of aromatic-aromatic interaction in inhibition.
Authors: Gao, X. / Wen, X. / Yu, C. / Esser, L. / Tsao, S. / Quinn, B. / Zhang, L. / Yu, L. / Xia, D.
History
DepositionMar 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Mar 3, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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_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 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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, mitochondrial precursor
B: Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor
C: Cytochrome b
E: Cytochrome c1, heme protein, mitochondrial
D: Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]
G: Ubiquinol-cytochrome C reductase complex 14 kDa protein
I: Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C
F: Ubiquinol-cytochrome C reductase complex 11 kDa protein
K: Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]
H: Ubiquinol-cytochrome C reductase complex 7.2 kDa protein
J: Ubiquinol-cytochrome C reductase complex 6.4 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,15817
Polymers241,29311
Non-polymers2,8646
Water5,188288
1
A: Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrial precursor
B: Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor
C: Cytochrome b
E: Cytochrome c1, heme protein, mitochondrial
D: Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]
G: Ubiquinol-cytochrome C reductase complex 14 kDa protein
I: Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C
F: Ubiquinol-cytochrome C reductase complex 11 kDa protein
K: Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]
H: Ubiquinol-cytochrome C reductase complex 7.2 kDa protein
J: Ubiquinol-cytochrome C reductase complex 6.4 kDa protein
hetero molecules

A: Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrial precursor
B: Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor
C: Cytochrome b
E: Cytochrome c1, heme protein, mitochondrial
D: Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]
G: Ubiquinol-cytochrome C reductase complex 14 kDa protein
I: Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C
F: Ubiquinol-cytochrome C reductase complex 11 kDa protein
K: Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]
H: Ubiquinol-cytochrome C reductase complex 7.2 kDa protein
J: Ubiquinol-cytochrome C reductase complex 6.4 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)488,31634
Polymers482,58722
Non-polymers5,72912
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area104510 Å2
ΔGint-699 kcal/mol
Surface area161660 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)154.385, 154.385, 590.271
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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Ubiquinol-cytochrome-c reductase complex core protein ... , 2 types, 2 molecules AB

#1: Protein Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrial precursor


Mass: 49266.254 Da / Num. of mol.: 1 / Fragment: core protein 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P31800, quinol-cytochrome-c reductase
#2: Protein Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor / Complex III subunit II


Mass: 46575.469 Da / Num. of mol.: 1 / Fragment: core protein 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P23004, quinol-cytochrome-c reductase

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Protein , 2 types, 2 molecules CE

#3: Protein Cytochrome b /


Mass: 42620.340 Da / Num. of mol.: 1 / Fragment: cytochrome b / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00157
#4: Protein Cytochrome c1, heme protein, mitochondrial / / Cytochrome c-1


Mass: 21640.580 Da / Num. of mol.: 1 / Fragment: cytochrome c1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13272

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Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ... , 2 types, 2 molecules DK

#5: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]


Mass: 27323.277 Da / Num. of mol.: 1 / Fragment: iron sulfur protein / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00125
#9: Protein Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske iron-sulfur protein) (RISP) [Contains: Ubiquinol-cytochrome c reductase 8 kDa protein (Complex III subunit IX)]


Mass: 6527.604 Da / Num. of mol.: 1 / Fragment: subunit 9 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07552

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Ubiquinol-cytochrome C reductase complex ... , 5 types, 5 molecules GIFHJ

#6: Protein Ubiquinol-cytochrome C reductase complex 14 kDa protein / Complex III subunit VI


Mass: 9606.027 Da / Num. of mol.: 1 / Fragment: subunit 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13271, quinol-cytochrome-c reductase
#7: Protein Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C / Ubiquinol-cytochrome C reductase complex 9.5 kDa protein / Complex III subunit VII


Mass: 7964.259 Da / Num. of mol.: 1 / Fragment: subunit 7 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13272, quinol-cytochrome-c reductase
#8: Protein Ubiquinol-cytochrome C reductase complex 11 kDa protein / Mitochondrial hinge protein / Cytochrome C1 / nonheme 11 kDa protein / Complex III subunit VIII


Mass: 13371.190 Da / Num. of mol.: 1 / Fragment: subunit 8 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00129, quinol-cytochrome-c reductase
#10: Protein Ubiquinol-cytochrome C reductase complex 7.2 kDa protein / Cytochrome C1 / nonheme 7 kDa protein / Complex III subunit X


Mass: 9189.116 Da / Num. of mol.: 1 / Fragment: subunit 10 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00126, quinol-cytochrome-c reductase
#11: Protein Ubiquinol-cytochrome C reductase complex 6.4 kDa protein / Complex III subunit XI


Mass: 7209.311 Da / Num. of mol.: 1 / Fragment: subunit 11 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00130, quinol-cytochrome-c reductase

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Non-polymers , 5 types, 294 molecules

#12: Chemical ChemComp-UQ2 / UBIQUINONE-2


Mass: 318.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26O4
#13: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#14: Chemical ChemComp-SMA / STIGMATELLIN A


Mass: 514.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H42O7
#15: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


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


Mass: 18.015 Da / Num. of mol.: 288 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.2
Details: 20mM ammonium acetate, 20% glycerol, 12% PEG4000, 0.5M KCl, 0.1% diheptanoyl-phosphatidylcholine , pH 7.2, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 27, 2000 / Details: mirrors
RadiationMonochromator: SAGITTALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 115861 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1qcr

1qcr


Resolution: 2.6→40 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.896 / SU B: 12.79 / SU ML: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.471 / ESU R Free: 0.313 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28079 3133 3 %RANDOM
Rwork0.23317 ---
all0.23464 100126 --
obs0.23464 100126 94.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.491 Å2
Baniso -1Baniso -2Baniso -3
1-2.11 Å20 Å20 Å2
2--2.11 Å20 Å2
3----4.22 Å2
Refine analyzeLuzzati coordinate error free: 0.313 Å / Luzzati sigma a free: 0.268 Å
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16497 0 193 288 16978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02117504
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.98623724
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.76102090
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1230.22583
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213053
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1450.28143
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2707
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.340.410474
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6063.80116851
X-RAY DIFFRACTIONr_scbond_it3.38437027
X-RAY DIFFRACTIONr_scangle_it4.7954.56865
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.337 228
Rwork0.299 7267
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8176-0.1060.35861.1317-0.80781.7820.09350.00050.032-0.10020.01990.59710.071-0.6054-0.11340.3388-0.11810.00360.4712-0.00740.619732.013187.496192.7359
20.2107-0.01820.06160.9649-0.01051.01090.0689-0.09710.14140.1697-0.04740.2381-0.1813-0.3086-0.02150.336-0.130.11290.2206-0.00540.401149.009393.631114.8081
30.8142-0.2372-0.1051.55590.1681.79620.07630.0240.1736-0.1182-0.02060.1135-0.2611-0.1075-0.05570.2789-0.092-0.00050.0305-0.00680.26669.009104.606491.9011
41.0224-0.4912-0.1322.43760.17581.42520.03260.0513-0.0651-0.1925-0.00430.37390.1008-0.2021-0.02830.3216-0.0631-0.06710.09950.00890.283957.27686.668973.2481
50.74620.06380.11530.33290.74530.83370.0603-0.22020.05340.288-0.03110.0274-0.0775-0.0939-0.02920.6439-0.29570.07470.30280.03350.355364.832368.6987154.1021
6-4.498623.270718.389627.684510.495315.7638-1.4372-1.92370.0125-0.44250.0618-0.8513-1.33610.67241.37540.496-0.00120.0030.492-0.00380.493573.088855.7187165.1745
70.5852-1.4796-0.60174.18831.22251.6656-0.1033-0.2334-0.25960.81340.0274-0.30740.41580.10940.07590.9055-0.3506-0.11910.52850.12840.377681.611557.3697171.857
80.6286-0.1270.33950.60940.03992.19580.1171-0.2396-0.2390.343-0.0681-0.11390.2455-0.044-0.0490.6587-0.32940.02880.29280.11590.451964.810544.9793152.7291
90.7901-0.304-0.92640.07450.23178.11890.086-0.30890.01260.32350.01140.11960.2052-0.722-0.09740.7208-0.32950.20230.47760.04570.429345.395671.4412158.8534
101.7730.02120.24251.65760.03950.8972-0.0135-0.5748-0.12790.62560.03310.0920.0834-0.0397-0.01971.1642-0.30690.20530.98190.08540.466154.644167.2755192.4896
111.26350.31280.65950.69410.18683.12430.046-0.29520.05550.2842-0.14120.2448-0.0275-0.58820.09520.4514-0.18530.19950.37810.00090.519243.26982.2108141.493
124.5746-0.7979-0.7412.08550.13793.9286-0.1082-1.10640.38980.8560.07530.2809-0.1866-0.43710.03291.2581-0.28350.09220.9474-0.30450.615273.9209112.995187.7898
132.6719-1.0104-1.03261.28060.26081.12380.0335-0.2211-0.29780.1868-0.07490.20850.3452-0.16320.04140.4819-0.28420.02490.23090.03490.336859.028847.1423122.0728
140.20030.0793-0.18051.5109-1.53093.04790.0736-0.3038-0.12130.33140.03640.21640.1085-0.398-0.110.5378-0.3340.11730.43180.03480.466248.085354.6222144.4587
155.6343-4.3591-2.89578.375-0.37477.63060.2459-0.4856-0.7325-0.51080.07070.53420.2061-0.1733-0.31660.7751-0.33290.06330.83690.16340.82539.514140.7779193.6938
167.6601-7.3057-3.012825.2457-4.30573.65170.19230.53680.04910.3602-0.27270.03360.1951-0.47440.08040.732-0.33070.07080.79570.04510.622539.93949.8749187.1355
170000000000000000.4943000.494300.4943000
18-2.13942.95745.316611.9366.566416.07860.10620.20750.0732-0.7619-0.16480.5430.4405-1.74140.05860.5051-0.01020.01470.4989-0.02230.629260.685394.915788.5208
1916.77095.255810.14913.82210.788724.83920.5474-1.1389-0.1103-0.0092-0.85580.51280.6988-1.03520.30840.51060.03160.06910.5778-0.00130.718455.003280.844393.7779
20168.527846.0736-37.420131.419410.168353.049-0.45215.5654-2.3496-0.62940.5103-1.1693-0.1023-3.4298-0.05820.49590-0.00050.4958-0.00070.497147.45598.4254104.2871
211.40540.47840.42612.5743-0.19771.93350.0043-0.3276-0.07810.53670.10730.1865-0.5755-1.1065-0.11160.6714-0.14450.27930.7446-0.08650.615638.794288.8666160.5742
221.37130.5927-2.98853.9944-4.439913.42640.162-0.29230.17820.43460.0430.1894-0.772-0.7166-0.20490.6164-0.13290.05670.5205-0.16410.584552.3207104.4943147.7367
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2311 - 231
2X-RAY DIFFRACTION2AA232 - 446232 - 446
3X-RAY DIFFRACTION3BB17 - 23517 - 235
4X-RAY DIFFRACTION4BB236 - 439236 - 439
5X-RAY DIFFRACTION5CC3 - 1333 - 133
6X-RAY DIFFRACTION5CC173 - 264173 - 264
7X-RAY DIFFRACTION5CN - O381 - 382
9X-RAY DIFFRACTION7CC134 - 172134 - 172
10X-RAY DIFFRACTION8CC265 - 379265 - 379
11X-RAY DIFFRACTION9DE173 - 241173 - 241
12X-RAY DIFFRACTION10DE1 - 1721 - 172
13X-RAY DIFFRACTION10DP242
14X-RAY DIFFRACTION11ED1 - 711 - 71
15X-RAY DIFFRACTION12ED72 - 19672 - 196
16X-RAY DIFFRACTION13FH6 - 1106 - 110
17X-RAY DIFFRACTION14GF1 - 751 - 75
18X-RAY DIFFRACTION15HJ12 - 5212 - 52
19X-RAY DIFFRACTION16HJ53 - 7853 - 78
20X-RAY DIFFRACTION17HJ49 - 7849 - 78
21X-RAY DIFFRACTION18IG2 - 262 - 26
22X-RAY DIFFRACTION19IG27 - 5127 - 51
23X-RAY DIFFRACTION20IG52 - 5752 - 57
24X-RAY DIFFRACTION21JK2 - 612 - 61
25X-RAY DIFFRACTION22KI1 - 531 - 53

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