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- PDB-3cwb: Chicken Cytochrome BC1 Complex inhibited by an iodinated analogue... -

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Basic information

Entry
Database: PDB / ID: 3cwb
TitleChicken Cytochrome BC1 Complex inhibited by an iodinated analogue of the polyketide Crocacin-D
Components
  • (MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE ...) x 6
  • (MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN ...) x 2
  • Cytochrome b
  • MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN
KeywordsOXIDOREDUCTASE / Crocacin D / inhibitor design / structure-activity relationship / polyketide / fungicide / CYTOCHROME BC1 / MEMBRANE PROTEIN / HEME PROTEIN / RIESKE IRON SULFUR PROTEIN / CYTOCHROME B / CYTOCHROME C1 / COMPLEX III / MITOCHONDRIAL PROCESSING PROTEA UBIQUINONE / REDOX ENZYME / RESPIRATORY CHAIN / Electron transport / Heme / Inner membrane / Iron / Membrane / Metal-binding / Mitochondrion / Transmembrane / Transport
Function / homology
Function and homology information


Respiratory electron transport / quinol-cytochrome-c reductase / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / response to oxidative stress / oxidoreductase activity ...Respiratory electron transport / quinol-cytochrome-c reductase / mitochondrial respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / response to oxidative stress / oxidoreductase activity / heme binding / mitochondrion / metal ion binding / cytoplasm
Similarity search - Function
Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain I / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C ...Cytochrome Bc1 Complex; Chain I / Cytochrome Bc1 Complex; Chain I / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Ubiquinol-cytochrome C reductase hinge domain / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome c1, transmembrane anchor, C-terminal / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / 3-layer Sandwich / Cytochrome b / : / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / 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
AZIDE ION / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-ICX / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Unknown ligand / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer / Complex III subunit 9 ...AZIDE ION / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-ICX / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Unknown ligand / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer / Complex III subunit 9 / Cytochrome b-c1 complex subunit 6 / Mitochondrial ubiquinol-cytochrome-c reductase complex core protein 2 / Cytochrome b-c1 complex subunit 7 / Mitochondrial ubiquinol-cytochrome-c reductase complex core protein i / Cytochrome b-c1 complex subunit 8 / Cytochrome b / Cytochrome b-c1 complex subunit Rieske, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Rigid Body Refinement / Resolution: 3.51 Å
AuthorsHuang, L. / Cromartie, T. / Viner, R. / Crowley, P.J. / Berry, E.A.
Citation
Journal: Bioorg.Med.Chem. / Year: 2008
Title: The role of molecular modeling in the design of analogues of the fungicidal natural products crocacins A and D.
Authors: Crowley, P.J. / Berry, E.A. / Cromartie, T. / Daldal, F. / Godfrey, C.R. / Lee, D.W. / Phillips, J.E. / Taylor, A. / Viner, R.
#1: Journal: Nature / Year: 1998
Title: Electron transfer by domain movement in cytochrome bc1.
Authors: Zhang, Z. / Huang, L. / Shulmeister, V.M. / Chi, Y.I. / Kim, K.K. / Hung, L.W. / Crofts, A.R. / Berry, E.A. / Kim, S.H.
#2: Journal: J.Mol.Biol. / Year: 2005
Title: Binding of the respiratory chain inhibitor antimycin to the mitochondrial bc1 complex: a new crystal structure reveals an altered intramolecular hydrogen-bonding pattern.
Authors: Huang, L.S. / Cobessi, D. / Tung, E.Y. / Berry, E.A.
History
DepositionApr 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 29, 2014Group: Non-polymer description
Revision 1.3Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Aug 30, 2023Group: 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 / _chem_comp.pdbx_synonyms / _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: MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I
B: MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2
C: Cytochrome b
D: MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN
E: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR PROTEIN
F: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN
G: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C
H: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII
I: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, leader sequence
J: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN
N: MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I
O: MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2
P: Cytochrome b
Q: MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN
R: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR PROTEIN
S: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN
T: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C
U: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII
V: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, leader sequence
W: MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)481,89754
Polymers462,91620
Non-polymers18,98134
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area106980 Å2
ΔGint-706 kcal/mol
Surface area156630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)174.778, 182.663, 242.945
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a homodimer of hetero-11-mers. Subunit 11 is not essential for activity and is missing in our preparation. The asymmetric unit of this crystal form contains one copy of the biological unit, two copies each of 10 proteins. The deposited structure is the asymmetric unit.

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Components

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MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN ... , 2 types, 4 molecules ANBO

#1: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN I


Mass: 49503.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX31*PLUS
#2: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME-C REDUCTASE COMPLEX CORE PROTEIN 2


Mass: 46683.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX29*PLUS

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Protein , 2 types, 4 molecules CPDQ

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


Mass: 42622.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P18946
#4: Protein MITOCHONDRIAL CYTOCHROME C1, HEME PROTEIN


Mass: 26973.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken)

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MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE ... , 6 types, 12 molecules ERFSGTHUIVJW

#5: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR PROTEIN


Mass: 21506.188 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q5ZLR5*PLUS
#6: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 14 KDA PROTEIN


Mass: 13394.463 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX30*PLUS
#7: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE UBIQUINONE-BINDING PROTEIN QP-C


Mass: 9498.735 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX32*PLUS
#8: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 11 KDA PROTEIN, COMPLEX III SUBUNIT VIII


Mass: 9057.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX28*PLUS
#9: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT, leader sequence


Mass: 5211.173 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q5ZLR5
#10: Protein MITOCHONDRIAL UBIQUINOL-CYTOCHROME C REDUCTASE 7.2 KDA PROTEIN


Mass: 7005.963 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VX27*PLUS

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Sugars , 1 types, 6 molecules

#12: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 10 types, 44 molecules

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


Mass: 744.034 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C41H78NO8P / Comment: DOPE, phospholipid*YM
#13: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#14: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#15: Chemical ChemComp-ICX / methyl N-[(5Z)-6-({[4-(4-iodobenzyl)phenyl]carbonyl}amino)hex-5-enoyl]glycinate


Mass: 520.360 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H25IN2O4
#16: Chemical ChemComp-UQ / Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)-isomer


Mass: 863.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C59H90O4
#17: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#18: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#19: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#20: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#21: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUES 1-446 OF ENTITY 1 = 33-478 OF NCBI XM_414356.2; RESIDUES 1-441 OF ENTITY 2 = 17-457 OF ...RESIDUES 1-446 OF ENTITY 1 = 33-478 OF NCBI XM_414356.2; RESIDUES 1-441 OF ENTITY 2 = 17-457 OF NCBI XM_424611.2; RESIDUES 1-380 OF ENTITY 3 = 1-380 OF NCBI NC_001323.1; RESIDUES 1-196 OF ENTITY 5 = 77-272 OF NCBI NM_001005843.1; RESIDUES 1-110 OF ENTITY 6 = 2-111 OF NCBI XM_418347.2; RESIDUES 1-81 OF ENTITY 7 = 37-117 OF NCBI XM_414651.1; RESIDUES 1-77 OF ENTITY 8 = 2-78 OF NCBI XM_001235147.1; RESIDUES 1-76 OF ENTITY 9 = 1-76 OF NCBI NM_001005843.1 (NOTE THIS IS THE SAME GENE AS ENTITY 5); RESIDUES 1-56 OF ENTITY 10 = 8-63 OF NCBI XM_001234249.1. FOR ENTITY 4 , THERE IS NO ANNOTATED ORF COVERING THE SEQUENCE, BUT THE NUCLEOTIDE SEQUENCE IS AVAILABLE IN THREE ENTRIES: TRANSLATE BASES 250-543 OF NCBI BI390492 GIVES RESIDUES 1-98, TRANSLATE BASES 3-692 OF NCBI BX934107 GIVES RESIDUES 12-241, TRANSLATE BASES 3-656 OF NCBI BX929288 GIVES RESIDUES 24-241. AT PRESENT THE NCBI SEQUENCES CAN BE OBTAINED FROM THE URL: HTTP://WWW.NCBI.NLM.NIH.GOV/ENTREZ/VIEWER.FCGI?VAL=, WHERE IS THE NCBI NUMBER GIVEN ABOVE.

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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: 4.19 Å3/Da / Density % sol: 70.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 20MM KMES, 75MM NACL, 10% GLYCEROL, 6% PEG4000. Crystal soaked with the inhibitor and RbBr salt, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.741439, 1.239798, 0.920205
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 4, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.7414391
21.2397981
30.9202051
ReflectionResolution: 3.5→60 Å / Num. obs: 96135 / % possible obs: 92.1 % / Observed criterion σ(I): -2 / Redundancy: 2.9 % / Biso Wilson estimate: 56.3 Å2 / Rmerge(I) obs: 0.168 / Rsym value: 0.178 / Net I/σ(I): 5
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 2 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 0.8 / Rsym value: 0.99 / % possible all: 78.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: Rigid Body Refinement
Starting model: PDB ENTRY 1BCC AFTER FURTHER REFINEMENT

1bcc


Resolution: 3.51→21.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 7037765.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Three datasets were obtained at different wavelengths. Data reduction statistics are given for the second wavelength, 1.239798 A, except for R-merge which is from merging the three datasets. ...Details: Three datasets were obtained at different wavelengths. Data reduction statistics are given for the second wavelength, 1.239798 A, except for R-merge which is from merging the three datasets. Refinement was against the resulting single merged dataset. The purpose of the multiple wavelength data collection was to locate the iodine atom in the inhibitor (successful) and cation and anion (RbCl) binding sites (unsuccesful). Only the merged data is deposited. Entity 9 is mobile in the crystals, occupying two or more different position. Only the major position is modeled. Overall occupancy was refined for this domain resulting in occupancy less than 1.0 for chain E in its predominant position. Some of the lipid and detergent molecules also refined to occupancy less than 1.0.
RfactorNum. reflection% reflectionSelection details
Rfree0.319 4899 5.1 %RANDOM
Rwork0.285 ---
obs0.285 96135 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 12.8267 Å2 / ksol: 0.22 e/Å3
Displacement parametersBiso mean: 100 Å2
Baniso -1Baniso -2Baniso -3
1-29.42 Å20 Å20 Å2
2---28.84 Å20 Å2
3----0.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.7 Å0.6 Å
Luzzati d res low-10 Å
Luzzati sigma a0.87 Å0.77 Å
Refinement stepCycle: LAST / Resolution: 3.51→21.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31806 0 874 16 32696
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.622
X-RAY DIFFRACTIONc_scbond_it1.512
X-RAY DIFFRACTIONc_scangle_it2.642.5
LS refinement shellResolution: 3.51→3.58 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.417 284 5.5 %
Rwork0.423 4847 -
obs--79.3 %

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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