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- PDB-5okd: Crystal structure of bovine Cytochrome bc1 in complex with inhibi... -

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Basic information

Entry
Database: PDB / ID: 5okd
TitleCrystal structure of bovine Cytochrome bc1 in complex with inhibitor SCR0911.
Components
  • (Cytochrome b-c1 complex subunit ...) x 8
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
KeywordsELECTRON TRANSPORT / antimalarial inhibitor / Qi site binder
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 / ubiquinone binding / ubiquinol-cytochrome-c reductase activity / 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 / ubiquinone binding / ubiquinol-cytochrome-c reductase activity / 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
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 / 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 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome c1, transmembrane anchor, C-terminal / 3-layer Sandwich / Cytochrome b / : / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / 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
1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Chem-9XE / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PHOSPHATE ION / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Cytochrome c1, heme protein, mitochondrial ...1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Chem-9XE / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / PHOSPHATE ION / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 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 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 / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsAmporndanai, K. / O'Neill, P.M. / Hasnain, S.S. / Antonyuk, S.V.
CitationJournal: IUCrJ / Year: 2018
Title: X-ray and cryo-EM structures of inhibitor-bound cytochrome complexes for structure-based drug discovery.
Authors: Kangsa Amporndanai / Rachel M Johnson / Paul M O'Neill / Colin W G Fishwick / Alexander H Jamson / Shaun Rawson / Stephen P Muench / S Samar Hasnain / Svetlana V Antonyuk /
Abstract: Cytochrome , a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. ...Cytochrome , a dimeric multi-subunit electron-transport protein embedded in the inner mitochondrial membrane, is a major drug target for the treatment and prevention of malaria and toxoplasmosis. Structural studies of cytochrome from mammalian homologues co-crystallized with lead compounds have underpinned structure-based drug design to develop compounds with higher potency and selectivity. However, owing to the limited amount of cytochrome that may be available from parasites, all efforts have been focused on homologous cytochrome complexes from mammalian species, which has resulted in the failure of some drug candidates owing to toxicity in the host. Crystallographic studies of the native parasite proteins are not feasible owing to limited availability of the proteins. Here, it is demonstrated that cytochrome is highly amenable to single-particle cryo-EM (which uses significantly less protein) by solving the apo and two inhibitor-bound structures to ∼4.1 Å resolution, revealing clear inhibitor density at the binding site. Therefore, cryo-EM is proposed as a viable alternative method for structure-based drug discovery using both host and parasite enzymes.
History
DepositionJul 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 30, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jan 17, 2024Group: 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Cytochrome b-c1 complex subunit 8
H: Cytochrome b-c1 complex subunit 6, mitochondrial
I: Cytochrome b-c1 complex subunit Rieske, mitochondrial
J: Cytochrome b-c1 complex subunit 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,44633
Polymers246,89510
Non-polymers12,55023
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50960 Å2
ΔGint-345 kcal/mol
Surface area82040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.871, 209.871, 342.097
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

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Components

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Cytochrome b-c1 complex subunit ... , 8 types, 8 molecules ABEFGHIJ

#1: Protein Cytochrome b-c1 complex subunit 1, mitochondrial / Complex III subunit 1 / Core protein I / Ubiquinol-cytochrome-c reductase complex core protein 1


Mass: 52840.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P31800
#2: Protein Cytochrome b-c1 complex subunit 2, mitochondrial / Complex III subunit 2 / Core protein II / Ubiquinol-cytochrome-c reductase complex core protein 2


Mass: 48203.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P23004
#5: Protein Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / ...Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Rieske protein UQCRFS1 / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 21640.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13272, quinol-cytochrome-c reductase
#6: Protein Cytochrome b-c1 complex subunit 7 / Complex III subunit 7 / Complex III subunit VII / QP-C / Ubiquinol-cytochrome c reductase complex ...Complex III subunit 7 / Complex III subunit VII / QP-C / Ubiquinol-cytochrome c reductase complex 14 kDa protein


Mass: 13502.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00129
#7: Protein Cytochrome b-c1 complex subunit 8 / Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa ...Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa protein / Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C


Mass: 9737.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13271
#8: Protein Cytochrome b-c1 complex subunit 6, mitochondrial / Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / ...Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / Mitochondrial hinge protein / Ubiquinol-cytochrome c reductase complex 11 kDa protein


Mass: 10638.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00126
#9: Protein/peptide Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / ...Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Rieske protein UQCRFS1 / Ubiquinol-cytochrome c reductase iron-sulfur subunit


Mass: 4898.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P13272, quinol-cytochrome-c reductase
#10: Protein Cytochrome b-c1 complex subunit 9 / Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol- ...Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol-cytochrome c reductase complex 7.2 kDa protein


Mass: 7469.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00130

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Protein , 2 types, 2 molecules CD

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


Mass: 35343.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00125

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Sugars , 1 types, 1 molecules

#16: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 11 types, 104 molecules

#11: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#12: Chemical ChemComp-6PE / 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 410.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H33NO8P
#13: 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
#14: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#15: Chemical ChemComp-9XE / 7-methoxy-3-methyl-2-[5-[4-(trifluoromethyloxy)phenyl]pyridin-3-yl]-1~{H}-quinolin-4-one


Mass: 426.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H17F3N2O3
#17: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE / Discrete optimized protein energy


Mass: 744.034 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#18: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#19: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#20: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#21: Chemical ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Dimyristoylphosphatidylcholine


Mass: 678.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#22: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 4.41 Å3/Da / Density % sol: 72.08 % / Description: Bipyramidal red
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: Protein 40mg/mL with 1.6% HECAMEG; reservoir solution 50mM KPi pH 6.8, 100mM NaCl, 3mM NaN3, 10-13% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2017 / Details: mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→89 Å / Num. obs: 80268 / % possible obs: 99.5 % / Redundancy: 7.4 % / Biso Wilson estimate: 71.303 Å2 / CC1/2: 0.977 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.043 / Net I/σ(I): 12.3
Reflection shellResolution: 3.1→3.16 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.126 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4428 / CC1/2: 0.572 / Rpim(I) all: 0.655 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4d6t

4d6t


Resolution: 3.1→31.76 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / SU B: 37.897 / SU ML: 0.295 / Cross valid method: THROUGHOUT / ESU R: 0.821 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23993 4037 5 %RANDOM
Rwork0.20462 ---
obs0.20641 76127 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 101.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.02 Å20 Å2
2--0.03 Å20 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 3.1→31.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15787 0 601 82 16470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01916779
X-RAY DIFFRACTIONr_bond_other_d0.0020.0215928
X-RAY DIFFRACTIONr_angle_refined_deg1.261.99322770
X-RAY DIFFRACTIONr_angle_other_deg0.887336616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84952005
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40823.338716
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.124152649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.12215109
X-RAY DIFFRACTIONr_chiral_restr0.0660.22475
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02118587
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023865
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1136.1088053
X-RAY DIFFRACTIONr_mcbond_other1.1136.1088052
X-RAY DIFFRACTIONr_mcangle_it1.9519.1610047
X-RAY DIFFRACTIONr_mcangle_other1.9519.1610048
X-RAY DIFFRACTIONr_scbond_it1.1966.4238725
X-RAY DIFFRACTIONr_scbond_other1.1966.4218722
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.089.53812716
X-RAY DIFFRACTIONr_long_range_B_refined4.60348.69618132
X-RAY DIFFRACTIONr_long_range_B_other4.60448.70118133
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 314 -
Rwork0.325 5522 -
obs--99.81 %
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)
11.6758-0.23590.03181.6119-0.34251.9048-0.11170.47240.6031-0.1550.088-0.1695-0.27430.08590.02370.0787-0.0731-0.03980.26690.33560.4928-92.594-30.256.856
21.3658-0.7633-0.44771.81830.17061.0939-0.02410.41240.3062-0.23790.01810.3782-0.2264-0.24440.00610.1117-0.0219-0.13420.33270.27040.4521-122.565-40.626.83
31.4233-0.8235-0.65832.14660.37650.8356-0.1706-0.0650.03460.40290.1673-0.26180.15760.26810.00320.11270.0736-0.11320.20690.00840.2408-56.694-71.47642.047
42.0218-0.27830.45680.7076-0.20260.5618-0.2216-0.02830.20870.20990.1563-0.6460.00170.4690.06520.12070.1887-0.15670.7622-0.13280.7824-28.079-73.87230.262
52.1697-2.4832-0.92553.73281.21561.02920.04690.51-0.3453-0.4363-0.03930.03960.26730.2371-0.00760.3734-0.01420.08090.8082-0.12270.6466-43.148-84.6352.416
63.42670.9544-0.88222.5143-1.30192.75660.0182-0.48170.49260.56610.0867-0.041-0.16570.0667-0.10480.24990.0721-0.05860.0933-0.08910.264-80.701-46.13552.213
72.9194-1.02351.79161.2088-1.04252.3976-0.09220.25050.42850.368-0.1295-0.66350.0020.76590.22170.29770.0538-0.21550.3651-0.09410.5522-53.392-50.52144.483
81.9721.3455-1.5640.9911-0.93915.59380.1229-0.2132-0.18040.2386-0.1846-0.3152-0.43850.72050.06170.52850.0674-0.40570.9885-0.08861.1073-11.18-62.91451.464
90.58321.13191.32642.66522.93723.3267-0.13210.11760.0659-0.01710.5015-0.3978-0.20780.4251-0.36940.6724-0.05990.00380.89840.06561.0742-109.53-38.04214.509
106.3698-3.16292.06883.1764-0.48171.37150.25230.720.365-0.4082-0.0798-0.5084-0.15010.3657-0.17250.1744-0.06250.16460.62640.17620.3933-43.213-56.7967.673
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 503
2X-RAY DIFFRACTION2B20 - 439
3X-RAY DIFFRACTION3C2 - 508
4X-RAY DIFFRACTION4D2 - 505
5X-RAY DIFFRACTION5E1 - 504
6X-RAY DIFFRACTION6F11 - 501
7X-RAY DIFFRACTION7G2 - 503
8X-RAY DIFFRACTION8H13 - 77
9X-RAY DIFFRACTION9I32 - 80
10X-RAY DIFFRACTION10J2 - 60

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