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- PDB-1sqq: Crystal Structure Analysis of Bovine Bc1 with Methoxy Acrylate St... -

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Basic information

Entry
Database: PDB / ID: 1sqq
TitleCrystal Structure Analysis of Bovine Bc1 with Methoxy Acrylate Stilbene (MOAS)
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


Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / Respiratory electron transport / thalamus development / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity ...Complex III assembly / subthalamus development / pons development / cerebellar Purkinje cell layer development / pyramidal neuron development / Respiratory electron transport / thalamus development / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / hypothalamus development / midbrain development / ubiquinone binding / respiratory electron transport chain / hippocampus development / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / mitochondrial inner membrane / heme binding / mitochondrion / proteolysis / metal ion binding / membrane
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 / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome c1, transmembrane anchor, C-terminal ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / 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 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Cytochrome b-c1 complex subunit 9 / 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 / : / 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] domain / Rieske [2Fe-2S] iron-sulphur 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 / Chem-OST / 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 / Chem-OST / 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 (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 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 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: Cytochrome c1, heme protein, mitochondrial
E: 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)]
F: Ubiquinol-cytochrome c reductase complex 14 kDa protein
G: Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C
H: Ubiquinol-cytochrome c reductase complex 11 kDa protein
I: 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)]
J: Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
K: Ubiquinol-cytochrome c reductase complex 6.4 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,93817
Polymers241,29311
Non-polymers2,6446
Water3,279182
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
D: Cytochrome c1, heme protein, mitochondrial
E: 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)]
F: Ubiquinol-cytochrome c reductase complex 14 kDa protein
G: Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C
H: Ubiquinol-cytochrome c reductase complex 11 kDa protein
I: 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)]
J: Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
K: 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
D: Cytochrome c1, heme protein, mitochondrial
E: 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)]
F: Ubiquinol-cytochrome c reductase complex 14 kDa protein
G: Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C
H: Ubiquinol-cytochrome c reductase complex 11 kDa protein
I: 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)]
J: Ubiquinol-cytochrome c reductase complex 7.2 kDa protein
K: Ubiquinol-cytochrome c reductase complex 6.4 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)487,87534
Polymers482,58722
Non-polymers5,28812
Water39622
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area102110 Å2
ΔGint-660 kcal/mol
Surface area164760 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)153.677, 153.677, 598.824
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 (domestic 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 (domestic cattle) / References: UniProt: P23004, quinol-cytochrome-c reductase

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Protein , 2 types, 2 molecules CD

#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 (domestic cattle) / References: UniProt: P00157
#4: Protein Cytochrome c1, heme protein, mitochondrial / Cytochrome c-1


Mass: 27323.277 Da / Num. of mol.: 1 / Fragment: cytochrome c1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00125

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

#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: 21640.580 Da / Num. of mol.: 1 / Fragment: iron sulfur protein / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13272
#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: 7964.259 Da / Num. of mol.: 1 / Fragment: subunit 9 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13272

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Ubiquinol-cytochrome c reductase complex ... , 5 types, 5 molecules FGHJK

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


Mass: 13371.190 Da / Num. of mol.: 1 / Fragment: subunit 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00129, 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: 9606.027 Da / Num. of mol.: 1 / Fragment: subunit 7 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13271, 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: 9189.116 Da / Num. of mol.: 1 / Fragment: subunit 8 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00126, 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: 7209.311 Da / Num. of mol.: 1 / Fragment: subunit 10 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00130, quinol-cytochrome-c reductase
#11: Protein Ubiquinol-cytochrome c reductase complex 6.4 kDa protein / Complex III subunit XI


Mass: 6527.604 Da / Num. of mol.: 1 / Fragment: subunit 11 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P07552, quinol-cytochrome-c reductase

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Non-polymers , 5 types, 188 molecules

#12: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#13: Chemical ChemComp-UQ2 / UBIQUINONE-2


Mass: 318.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26O4
#14: Chemical ChemComp-OST / METHYL (2Z)-3-METHOXY-2-{2-[(E)-2-PHENYLVINYL]PHENYL}ACRYLATE


Mass: 294.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18O3
#15: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.41 %
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: NSLS / Beamline: X9B / Wavelength: 1.736 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 21, 2001 / Details: mirrors
RadiationMonochromator: SAGITTALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.736 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 67802 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 3→3.08 Å / % possible all: 90.2

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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: 3→50 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.876 / SU B: 18.766 / SU ML: 0.352 / Cross valid method: THROUGHOUT / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29485 2113 3 %RANDOM
Rwork0.22815 ---
obs0.2302 67802 96.84 %-
all-67802 --
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: 27.643 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å20 Å2
2--2.01 Å20 Å2
3----4.02 Å2
Refine analyzeLuzzati coordinate error free: 0.458 Å / Luzzati sigma a free: 0.357 Å
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16527 0 178 182 16887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02117551
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.98423785
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg21.105102093
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_restr0.1690.22590
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0213067
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1810.28600
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2679
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.292
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5080.410484
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4063.80116868
X-RAY DIFFRACTIONr_scbond_it5.09937064
X-RAY DIFFRACTIONr_scangle_it7.5124.56909
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.079 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.417 135
Rwork0.301 4948
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)
10.78160.04860.60911.1362-1.15171.93730.0794-0.01540.1139-0.10420.08450.63250.0313-0.6842-0.16390.3647-0.08080.0310.4905-0.02270.60231.597887.107294.2101
20.1585-0.2274-0.05071.548-0.03530.74590.058-0.06760.20010.1837-0.06140.2604-0.116-0.26510.00350.3513-0.15230.1180.2504-0.02570.319448.650893.3883116.1592
30.7835-0.29060.19631.93850.1951.90560.08010.0680.2415-0.144600.0678-0.305-0.147-0.08010.2516-0.09840.00570.03890.00640.194368.6841104.324893.1372
41.233-0.82060.092.743-0.04491.33040.03660.0439-0.0761-0.24470.01720.39270.0469-0.2332-0.05380.2616-0.0711-0.06660.1275-0.00930.263656.856486.266374.6031
50.7911-0.05820.32740.32950.85550.7590.1344-0.35810.02770.3844-0.1065-0.0019-0.0559-0.139-0.02790.7258-0.34730.07910.37760.02710.291764.571368.6239155.5975
6-0.41360.8260.36920.21660.19262.66620.011-0.56730.18580.6155-0.0231-0.4750.11740.44590.01211.0185-0.3579-0.13450.63370.15550.572480.907256.5542173.7292
71.1971-0.04320.1860.46670.32522.73430.1847-0.3943-0.11790.3617-0.0137-0.08060.25970.0974-0.1710.7336-0.36050.03780.34720.09720.432964.600345.036154.4328
80000000000000000.5582000.558200.5582000
90.6535-0.1539-1.2480.2459-0.52315.06470.0992-0.29570.03170.4392-0.05790.1781-0.141-0.5479-0.04140.8108-0.37590.21780.48570.0140.427245.001271.5107160.5007
101.41350.17650.34492.30350.71981.5847-0.0231-0.4659-0.14260.70630.0972-0.03030.1011-0.1373-0.07411.3853-0.41970.22541.1490.06480.566954.285767.5365194.0892
111.44250.99211.59181.41641.88273.81770.2378-0.38950.08440.3148-0.17610.18940.0412-0.7332-0.06170.5616-0.22720.26160.4723-0.02340.493743.032582.0168142.8662
1210.1382.5693-1.591916.00893.281412.7893-0.04690.15070.67010.08110.1289-0.43820.09-0.1659-0.0821.14710.0009-0.03391.3352-0.18831.087970.6374111.4253190.7281
133.6504-1.1415-1.09871.5134-0.01621.1313-0.0619-0.2394-0.36790.20230.01210.21750.4495-0.18540.04980.536-0.30360.02150.23930.01960.246258.71346.9066123.5702
140.18150.098-0.30040.8799-1.02032.67320.0586-0.4236-0.07970.3723-0.06540.0970.1719-0.23590.00680.607-0.35080.11710.48610.06440.461447.824554.6462146.0128
154.6235-3.5586-2.28596.98171.17267.0140.3171-0.3303-0.3172-0.1475-0.3210.17990.0498-0.42250.00390.8667-0.33030.0690.99490.17540.839739.006141.9344196.5194
166.8395-11.5247-4.547225.1133-2.23197.0006-0.1540.0971-0.0240.16660.15580.02670.4156-0.7861-0.00180.8541-0.34940.1140.872-0.05440.72539.558949.9336188.8704
170000000000000000.5582000.558200.5582000
185.6314.28567.75044.18946.206712.853-0.30280.5225-0.014-0.1699-0.58040.58360.0108-2.37720.88310.5751-0.01050.14610.5463-0.15990.614160.38594.728789.6323
1911.21-1.82769.78155.4812-4.361313.47330.8395-0.5424-0.48120.2137-0.31830.291.0112-0.6452-0.52120.61230.04070.07570.7232-0.06690.732654.356580.750894.9735
20117.3058-7.0285-28.927348.215520.605126.6496-2.64445.3556-0.4295-0.50231.85550.58550.4177-0.92370.78880.5586-0.0005-0.00410.5589-0.00790.561846.783298.4128105.1981
212.07390.96210.00033.0287-0.6255.33010.1458-0.521-0.00040.7560.00620.2389-0.5608-1.0718-0.1520.8261-0.0870.27540.7642-0.10310.580438.722689.1815162.5846
221.84081.5514-4.15314.7041-5.301716.910.0776-0.51390.10920.3560.0066-0.0395-0.2835-0.1179-0.08420.6603-0.1480.02810.575-0.23620.60852.1779104.1906149.6405
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 DIFFRACTION5CL - M381 - 382
8X-RAY DIFFRACTION6CC134 - 172134 - 172
9X-RAY DIFFRACTION7CC265 - 379265 - 379
10X-RAY DIFFRACTION8CL381
11X-RAY DIFFRACTION9DD173 - 241173 - 241
12X-RAY DIFFRACTION10DD1 - 1721 - 172
13X-RAY DIFFRACTION10DP242
14X-RAY DIFFRACTION11EE1 - 711 - 71
15X-RAY DIFFRACTION12EE72 - 19672 - 196
16X-RAY DIFFRACTION13FF6 - 1106 - 110
17X-RAY DIFFRACTION14GG1 - 751 - 75
18X-RAY DIFFRACTION15HH9 - 529 - 52
19X-RAY DIFFRACTION16HH53 - 7853 - 78
20X-RAY DIFFRACTION17HH49 - 7849 - 78
21X-RAY DIFFRACTION18II2 - 262 - 26
22X-RAY DIFFRACTION19II27 - 5127 - 51
23X-RAY DIFFRACTION20II52 - 5752 - 57
24X-RAY DIFFRACTION21JJ3 - 613 - 61
25X-RAY DIFFRACTION22KK1 - 541 - 54

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