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- PDB-6xvf: Crystal structure of bovine cytochrome bc1 in complex with tetrah... -

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Basic information

Entry
Database: PDB / ID: 6xvf
TitleCrystal structure of bovine cytochrome bc1 in complex with tetrahydro-quinolone inhibitor JAG021
Components
  • (Cytochrome b-c1 complex subunit ...) x 8
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
KeywordsMEMBRANE PROTEIN / Cytochrome bc1 / Malaria / 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
Ubiquinol cytochrome reductase, transmembrane domain / 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 ...Ubiquinol cytochrome reductase, transmembrane domain / 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 / 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 / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-JAG / 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 / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-JAG / 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 (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsAmporndanai, K. / Hasnain, S.S. / Antonyuk, S.V.
CitationJournal: Front Cell Infect Microbiol / Year: 2020
Title: Potent Tetrahydroquinolone Eliminates Apicomplexan Parasites.
Authors: Martin J McPhillie / Ying Zhou / Mark R Hickman / James A Gordon / Christopher R Weber / Qigui Li / Patty J Lee / Kangsa Amporndanai / Rachel M Johnson / Heather Darby / Stuart Woods / Zhu- ...Authors: Martin J McPhillie / Ying Zhou / Mark R Hickman / James A Gordon / Christopher R Weber / Qigui Li / Patty J Lee / Kangsa Amporndanai / Rachel M Johnson / Heather Darby / Stuart Woods / Zhu-Hong Li / Richard S Priestley / Kurt D Ristroph / Scott B Biering / Kamal El Bissati / Seungmin Hwang / Farida Esaa Hakim / Sarah M Dovgin / Joseph D Lykins / Lucy Roberts / Kerrie Hargrave / Hua Cong / Anthony P Sinai / Stephen P Muench / Jitender P Dubey / Robert K Prud'homme / Hernan A Lorenzi / Giancarlo A Biagini / Silvia N Moreno / Craig W Roberts / Svetlana V Antonyuk / Colin W G Fishwick / Rima McLeod /
Abstract: Apicomplexan infections cause substantial morbidity and mortality, worldwide. New, improved therapies are needed. Herein, we create a next generation anti-apicomplexan lead compound, JAG21, a ...Apicomplexan infections cause substantial morbidity and mortality, worldwide. New, improved therapies are needed. Herein, we create a next generation anti-apicomplexan lead compound, JAG21, a tetrahydroquinolone, with increased sp3-character to improve parasite selectivity. Relative to other cytochrome inhibitors, JAG21 has improved solubility and ADMET properties, without need for pro-drug. JAG21 significantly reduces tachyzoites and encysted bradyzoites , and in primary and established chronic murine infections. Moreover, JAG21 treatment leads to 100% survival. Further, JAG21 is efficacious against drug-resistant . Causal prophylaxis and radical cure are achieved after sporozoite infection with oral administration of a single dose (2.5 mg/kg) or 3 days treatment at reduced dose (0.625 mg/kg/day), eliminating parasitemia, and leading to 100% survival. Enzymatic, binding, and co-crystallography/pharmacophore studies demonstrate selectivity for apicomplexan relative to mammalian enzymes. JAG21 has significant promise as a pre-clinical candidate for prevention, treatment, and cure of toxoplasmosis and malaria.
History
DepositionJan 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 2.0Jan 24, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.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)238,21636
Polymers225,39110
Non-polymers12,82426
Water34219
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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

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)476,43172
Polymers450,78320
Non-polymers25,64952
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area111480 Å2
ΔGint-785 kcal/mol
Surface area150770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.869, 209.869, 342.418
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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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: 49165.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic 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: 44495.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic 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 (domestic 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: 12485.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic 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: 8799.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic 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: 7515.433 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic 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: 4827.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic 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: 6866.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic 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: 42489.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic 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: 27107.021 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic 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, 44 molecules

#11: Chemical ChemComp-PG4 / TETRAETHYLENE 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#14: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#15: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#17: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#18: Chemical ChemComp-JAG / 2-methyl-3-[4-[4-(trifluoromethyloxy)phenoxy]phenyl]-5,6,7,8-tetrahydro-3~{H}-quinolin-4-one


Mass: 415.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H20F3NO3 / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#20: Chemical ChemComp-FES / FE2/S2 (INORGANIC) 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


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


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

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Details

Has ligand of interestY

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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: 4.86 Å3/Da / Density % sol: 74.7 % / Description: Bipyramidal red crystals
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 1, 2017 / Details: mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.45→90.88 Å / Num. obs: 53526 / % possible obs: 91.4 % / Redundancy: 11.4 % / Biso Wilson estimate: 94.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.225 / Rpim(I) all: 0.068 / Rrim(I) all: 0.235 / Net I/σ(I): 8.6
Reflection shellResolution: 3.45→3.56 Å / Redundancy: 11.6 % / Rmerge(I) obs: 1.111 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4659 / CC1/2: 0.295 / Rpim(I) all: 0.334 / % possible all: 92.8

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Processing

Software
NameVersionClassification
Aimless0.6.3data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
iMOSFLM7.2.2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OKD

5okd


Resolution: 3.5→90.88 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.911 / SU B: 0.584 / SU ML: 0.374 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.493 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 2583 5 %RANDOM
Rwork0.2174 ---
obs0.2181 48681 90.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 304.39 Å2 / Biso mean: 165.129 Å2 / Biso min: 28.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å20 Å2
2---0.09 Å20 Å2
3---0.3 Å2
Refinement stepCycle: final / Resolution: 3.5→90.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15505 0 597 19 16121
Biso mean--178.75 59.81 -
Num. residues----2006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01916490
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.99122401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7251994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26123.343691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.312152510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.39215102
X-RAY DIFFRACTIONr_chiral_restr0.0910.22442
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112373
LS refinement shellResolution: 3.5→3.591 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.326 194 -
Rwork0.309 3577 -
obs--92.09 %
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)
10.5875-0.39120.07650.9601-0.15440.4632-0.09060.26220.27290.07920.0085-0.1320.00190.08410.08210.3553-0.0573-0.040.51770.3690.8865-93.0289-30.62126.9876
20.5878-0.1767-0.30240.70510.07170.549-0.08630.26360.21440.03180.07650.21940.0693-0.11380.00980.34180.0146-0.11690.60850.27310.8222-122.6523-40.52857.2459
30.5058-0.3119-0.04410.45020.03050.2559-0.1220.12360.12620.23230.1043-0.10520.0670.14330.01770.4480.1218-0.09690.62080.01760.7436-56.8492-71.055141.8394
40.87540.46880.01590.32180.0560.2203-0.11290.18030.07690.01350.1728-0.20710.0570.3967-0.05990.09640.1607-0.17180.8572-0.04541.0077-27.9861-73.950830.1934
51.2447-1.5099-0.6212.45830.90040.4872-0.17110.20860.02380.08370.1550.21090.11860.23860.01610.25420.07220.09960.8518-0.03350.7215-43.9349-83.42942.7617
60.9930.3028-0.21460.849-0.97521.3249-0.1762-0.07450.44820.15640.1838-0.07550.0284-0.1519-0.00760.60190.1028-0.11960.3991-0.07050.8158-80.8042-46.23752.147
71.756-0.45230.53770.21240.06360.6476-0.1034-0.13160.62130.11250.0667-0.16570.11130.08350.03670.4136-0.0986-0.21520.46870.06180.8753-56.429-48.989242.5445
81.466-0.5864-0.70520.27150.38370.6899-0.24460.0386-0.0055-0.00910.0858-0.0264-0.28120.41380.15880.6216-0.3162-0.56840.8391-0.0631.3982-11.5604-62.934251.4932
91.1754-0.1813-0.82940.03390.15280.71170.04590.08680.2034-0.03040.05890.0021-0.08560.2456-0.10480.4898-0.1076-0.20260.76850.17460.8842-110.2086-37.562214.4388
100.8411-0.5864-0.0561.53080.23040.05420.14120.86080.2743-0.2043-0.076-0.2041-0.0580.0805-0.06510.09020.02730.12411.26850.26130.7276-43.5097-56.74817.7661
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 502
2X-RAY DIFFRACTION2B22 - 439
3X-RAY DIFFRACTION3C2 - 409
4X-RAY DIFFRACTION4D2 - 503
5X-RAY DIFFRACTION5E1 - 205
6X-RAY DIFFRACTION6F11 - 501
7X-RAY DIFFRACTION7G2 - 103
8X-RAY DIFFRACTION8H14 - 77
9X-RAY DIFFRACTION9I33 - 78
10X-RAY DIFFRACTION10J2 - 60

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