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- PDB-3eh5: Structure of the reduced form of cytochrome ba3 oxidase from Ther... -

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Basic information

Entry
Database: PDB / ID: 3eh5
TitleStructure of the reduced form of cytochrome ba3 oxidase from Thermus thermophilus
Components
  • (Cytochrome c oxidase subunit ...) x 2
  • Cytochrome c oxidase polypeptide 2A
KeywordsOXIDOREDUCTASE / CYTOCHROME BA3 OXIDASE / HEME / INTEGRAL MEMBRANE PROTEIN / COPPER / ELECTRON TRANSPORT / HYDROGEN ION TRANSPORT / ION TRANSPORT / IRON / METAL-BINDING / RESPIRATORY CHAIN / TRANSMEMBRANE / TRANSPORT / FORMYLATION / Cell membrane / Membrane
Function / homology
Function and homology information


cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / respirasome / copper ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome c oxidase polypeptide 2A / Cytochrome c oxidase polypeptide 2A, ba3 type / Cytochrome c oxidase subunit IIa family / Ba3-like heme-copper oxidase subunit I / Cytochrome C oxidase subunit IIa, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane / Ba3-like heme-copper oxidase subunit II, C-terminal / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Copper centre Cu(A) ...Cytochrome c oxidase polypeptide 2A / Cytochrome c oxidase polypeptide 2A, ba3 type / Cytochrome c oxidase subunit IIa family / Ba3-like heme-copper oxidase subunit I / Cytochrome C oxidase subunit IIa, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane / Ba3-like heme-copper oxidase subunit II, C-terminal / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cupredoxins - blue copper proteins / Cupredoxin / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (I) ION / DINUCLEAR COPPER ION / HEME-AS / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c oxidase polypeptide 2A / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLiu, B. / Chen, Y. / Doukov, T. / Soltis, S.M. / Stout, D. / Fee, J.A.
Citation
Journal: Biochemistry / Year: 2009
Title: Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the ...Title: Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme.
Authors: Liu, B. / Chen, Y. / Doukov, T. / Soltis, S.M. / Stout, C.D. / Fee, J.A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus
Authors: Liu, B. / Luna, M. / Chen, Y. / Stout, D. / Fee, J.A.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: A novel cryoprotection scheme for enhancing the diffraction of crystals of recombinant cytochrome ba3 oxidase from Thermus thermophilus
Authors: Hunsicker-Wang, L.M. / Pacoma, R.L. / Chen, Y. / Fee, J.A. / Stout, C.D.
History
DepositionSep 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase polypeptide 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,93011
Polymers90,9763
Non-polymers2,9548
Water1,49583
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14180 Å2
ΔGint-145 kcal/mol
Surface area26490 Å2
MethodPISA
2
A: Cytochrome c oxidase subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5087
Polymers68,9871
Non-polymers2,5206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4772
Polymers18,3501
Non-polymers1271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Cytochrome c oxidase polypeptide 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9452
Polymers3,6381
Non-polymers3061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.631, 115.631, 149.169
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Cytochrome c oxidase subunit ... , 2 types, 2 molecules AB

#1: Protein Cytochrome c oxidase subunit 1 / / Cytochrome c oxidase polypeptide I / Cytochrome c ba(3) subunit I / Cytochrome cba3 subunit 1


Mass: 68987.453 Da / Num. of mol.: 1 / Fragment: UNP residues 2-562 / Mutation: K258R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: cbaA, TTHA1135 / Plasmid: PMK18 / Production host: THERMUS THERMOPHILUS (bacteria) / Strain (production host): HB8 / References: UniProt: Q5SJ79, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 / / Cytochrome c oxidase polypeptide II / Cytochrome c ba(3) subunit II / Cytochrome cba3 subunit 2


Mass: 18349.990 Da / Num. of mol.: 1 / Fragment: UNP residues 3-168 / Mutation: E4Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: cbaB, ctaC, TTHA1134 / Plasmid: PMK18 / Production host: THERMUS THERMOPHILUS (bacteria) / Strain (production host): HB8 / References: UniProt: Q5SJ80, cytochrome-c oxidase

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Protein/peptide / Sugars , 2 types, 5 molecules C

#3: Protein/peptide Cytochrome c oxidase polypeptide 2A / Cytochrome c oxidase polypeptide IIA / Cytochrome c ba(3) subunit IIA / Cytochrome cba3 subunit 2A


Mass: 3638.407 Da / Num. of mol.: 1 / Fragment: UNP residues 2-34
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: cbaD, TTHA1133 / Plasmid: PMK18 / Production host: THERMUS THERMOPHILUS (bacteria) / Strain (production host): HB8 / References: UniProt: P82543, cytochrome-c oxidase
#7: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 87 molecules

#4: Chemical ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-HAS / HEME-AS


Mass: 920.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H64FeN4O6
#8: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Peg 2000, Bis-tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.979 Å
DetectorType: ADSC Quantum-315R CCD / Detector: Q315R / Date: Jul 27, 2007
Details: Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing).
RadiationMonochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.55→20 Å / Num. obs: 33534 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 6.3
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 0.9 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XME

1xme


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 27.09 / SU ML: 0.286 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1274 5 %RANDOM
Rwork0.19656 ---
obs0.19959 24159 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 89.502 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5966 0 195 83 6244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226373
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1532.0018748
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8955753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33522.213235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.11815909
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0371529
X-RAY DIFFRACTIONr_chiral_restr0.1350.2981
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024778
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2660.23507
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3270.24215
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0870.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3590.2125
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6823876
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.75646089
X-RAY DIFFRACTIONr_scbond_it3.41843001
X-RAY DIFFRACTIONr_scangle_it4.56562655
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 100 -
Rwork0.233 1734 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -28.42 Å / Origin y: 22.384 Å / Origin z: -0.441 Å
111213212223313233
T0.031 Å20.0421 Å20.0055 Å2-0.0387 Å2-0.0516 Å2---0.1331 Å2
L0.9024 °2-0.4889 °2-0.6118 °2-0.9952 °20.6083 °2--0.9103 °2
S-0.0681 Å °-0.1524 Å °0.1201 Å °0.0853 Å °0.2098 Å °-0.0962 Å °0.1344 Å °0.1922 Å °-0.1417 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 562
2X-RAY DIFFRACTION1B3 - 168
3X-RAY DIFFRACTION1C2 - 34

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