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- PDB-2bcc: STIGMATELLIN-BOUND CYTOCHROME BC1 COMPLEX FROM CHICKEN -

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Basic information

Entry
Database: PDB / ID: 2bcc
TitleSTIGMATELLIN-BOUND CYTOCHROME BC1 COMPLEX FROM CHICKEN
Components(UBIQUINOL CYTOCHROME C ...) x 10
KeywordsOXIDOREDUCTASE / UBIQUINONE / REDOX ENZYME / MEMBRANE PROTEIN / RESPIRATORY CHAIN / STIGMATELLIN
Function / homology
Function and homology information


Respiratory electron transport / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain ...Respiratory electron transport / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respiratory chain complex III / mitochondrial respiratory chain complex IV / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / metalloendopeptidase activity / mitochondrial inner membrane / response to oxidative stress / oxidoreductase activity / heme binding / mitochondrion / proteolysis / metal ion binding / cytoplasm
Similarity search - Function
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 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 / Cytochrome c1, transmembrane anchor, C-terminal / 3-layer Sandwich / Cytochrome b / : / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / STIGMATELLIN / UBIQUINONE-10 / 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-c1 complex subunit 8 ...FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / STIGMATELLIN / UBIQUINONE-10 / 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-c1 complex subunit 8 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT USING NATIVE STRUCTURE SOLVED BY THE SAME AUTHOR / Resolution: 3.5 Å
AuthorsZhang, Z. / Huang, L. / Shulmeister, V.M. / Chi, Y.I. / Kim, K.K. / Hung, L.W. / Crofts, A.R. / Berry, E.A. / Kim, S.H.
Citation
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.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Pathways for proton release during ubihydroquinone oxidation by the bc(1) complex.
Authors: Crofts, A.R. / Hong, S. / Ugulava, N. / Barquera, B. / Gennis, R. / Guergova-Kuras, M. / Berry, E.A.
History
DepositionSep 18, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 22, 2013Group: Database references
Revision 1.4Oct 29, 2014Group: Non-polymer description
Revision 1.5Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.6Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / 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 / _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.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Aug 23, 2023Group: Atomic model / Data collection ...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
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
Remark 300 BIOMOLECULE DETERGENT SOLUBILIZED ENZYME IS DIMERIC, SAME DIMERIC RELATIONSHIP IS FOUND IN ... BIOMOLECULE DETERGENT SOLUBILIZED ENZYME IS DIMERIC, SAME DIMERIC RELATIONSHIP IS FOUND IN DIFFERENT CRYSTAL FORMS, SOMETIMES ON CRYSTALLOGRAPHIC TWO-FOLD. THIS DIMERIC BIOMOLECULES IS PRESENT IN THE ASYMMETRIC UNIT, HOWEVER THIS PDB ENTRY DOES NOT CONTAIN THE ASYMMETRIC UNIT BUT ONLY ONE MONOMER. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE.
Remark 350 GENERATING THE BIOMOLECULE COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY ... GENERATING THE BIOMOLECULE COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J BIOMT1 1 -0.836106 -0.548567 -0.000520 130.10969 BIOMT2 1 -0.548555 0.836080 0.007595 38.18410 BIOMT3 1 -0.003732 0.006636 -0.999971 169.17245

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
B: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
C: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
D: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
E: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
F: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
G: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
H: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
I: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
J: UBIQUINOL CYTOCHROME C OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,09919
Polymers228,94810
Non-polymers5,1529
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.460, 182.450, 241.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: generate
Matrix: (-0.836106, -0.548567, -0.00052), (-0.548555, 0.83608, 0.007595), (-0.003732, 0.006636, -0.999971)
Vector: 130.1097, 38.1841, 169.17245)

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Components

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UBIQUINOL CYTOCHROME C ... , 10 types, 10 molecules ABCDEFGHIJ

#1: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 COMPLEX / COMPLEX III


Mass: 49795.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM TISSUE / Source: (natural) Gallus gallus (chicken)
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRIAMitochondrion / Tissue: MUSCLESkeletal muscle
References: UniProt: P31800*PLUS, quinol-cytochrome-c reductase
#2: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 COMPLEX / COMPLEX III


Mass: 45091.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM TISSUE / Source: (natural) Gallus gallus (chicken)
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRIAMitochondrion / Tissue: MUSCLESkeletal muscle
References: UniProt: P23004*PLUS, quinol-cytochrome-c reductase
#3: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 COMPLEX / COMPLEX III


Mass: 42622.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM TISSUE / Source: (natural) Gallus gallus (chicken)
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRIAMitochondrion / Tissue: MUSCLESkeletal muscle / References: UniProt: P18946, quinol-cytochrome-c reductase
#4: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 COMPLEX / COMPLEX III


Mass: 27357.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM TISSUE / Source: (natural) Gallus gallus (chicken)
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRIAMitochondrion / Tissue: MUSCLESkeletal muscle
References: UniProt: P00125*PLUS, quinol-cytochrome-c reductase
#5: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 COMPLEX / COMPLEX III


Mass: 21739.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM TISSUE / Source: (natural) Gallus gallus (chicken)
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRIAMitochondrion / Tissue: MUSCLESkeletal muscle
References: UniProt: P13272*PLUS, quinol-cytochrome-c reductase
#6: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 COMPLEX / COMPLEX III


Mass: 13400.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM TISSUE / Source: (natural) Gallus gallus (chicken)
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRIAMitochondrion / Tissue: MUSCLESkeletal muscle
References: UniProt: P00129*PLUS, quinol-cytochrome-c reductase
#7: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 COMPLEX / COMPLEX III


Mass: 9715.241 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM TISSUE / Source: (natural) Gallus gallus (chicken)
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRIAMitochondrion / Tissue: MUSCLESkeletal muscle
References: UniProt: P13271*PLUS, quinol-cytochrome-c reductase
#8: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 COMPLEX / COMPLEX III


Mass: 9223.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM TISSUE / Source: (natural) Gallus gallus (chicken)
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRIAMitochondrion / Tissue: MUSCLESkeletal muscle
References: UniProt: P00126*PLUS, quinol-cytochrome-c reductase
#9: Protein/peptide UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 COMPLEX / COMPLEX III


Mass: 2826.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM TISSUE / Source: (natural) Gallus gallus (chicken)
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRIAMitochondrion / Tissue: MUSCLESkeletal muscle / References: quinol-cytochrome-c reductase
#10: Protein UBIQUINOL CYTOCHROME C OXIDOREDUCTASE / CYTOCHROME BC1 COMPLEX / COMPLEX III


Mass: 7175.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ISOLATED FROM TISSUE / Source: (natural) Gallus gallus (chicken)
Cellular location: MITOCHONDRIAL INNER MEMBRANEInner mitochondrial membrane
Organ: HEART / Organelle: MITOCHONDRIAMitochondrion / Tissue: MUSCLESkeletal muscle
References: UniProt: P00130*PLUS, quinol-cytochrome-c reductase

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Sugars , 1 types, 1 molecules

#15: 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.: 1
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 , 5 types, 8 molecules

#11: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#12: Chemical ChemComp-U10 / UBIQUINONE-10 / Coenzyme Q10 / Coenzyme Q10


Mass: 863.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C59H90O4
#13: 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
#14: Chemical ChemComp-SIG / STIGMATELLIN / Stigmatellin


Mass: 482.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H42O5 / Comment: inhibitor*YM
#16: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2

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Details

Sequence detailsTHOUGH PROTEINS IN THIS ENTRY ARE FROM CHICKEN, BOVINE SEQUENCES WERE USED FOR MODELING.

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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: 3.93 Å3/Da / Density % sol: 68.7 %
Crystal growpH: 6.7
Details: 20MM KMES PH6.7, 75MM NACL, 10% GLYCEROL, AND 6% PEG4000, INHIBITOR WAS ADDED FROM ETHANOLIC SOLUTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 4, 1997 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 3→10000 Å / Num. obs: 117928 / % possible obs: 77.1 % / Redundancy: 2.9 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 6
Reflection shellResolution: 3.38→3.56 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.459 / % possible all: 75

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
ALMNmodel building
TFFC(CCP4 PACKAGE)model building
RAVEmodel building
CNS0.1refinement
CCP4(ALMNphasing
TFFCphasing
RAVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT USING NATIVE STRUCTURE SOLVED BY THE SAME AUTHOR
Starting model: PDB 1BCC

1bcc


Resolution: 3.5→12 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.317 4034 5 %RANDOM
Rwork0.284 ---
obs0.284 80760 85.6 %-
Displacement parametersBiso mean: 4.6 Å2
Baniso -1Baniso -2Baniso -3
1--19.43 Å20 Å20 Å2
2--14.79 Å20 Å2
3---4.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.65 Å0.56 Å
Luzzati d res low-12 Å
Luzzati sigma a0.3 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 3.5→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15439 0 315 0 15754
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.5→3.71 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 621 5.3 %
Rwork0.329 11079 -
obs--75.1 %

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