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Basic information

Entry
Database: PDB / ID: 8hua
TitleSerial synchrotron crystallography structure of ba3-type cytochrome c oxidase from Thermus thermophilus using a goniometer compatible flow-cell
Components
  • (Cytochrome c oxidase subunit ...) x 2
  • Cytochrome c oxidase polypeptide 2A
KeywordsELECTRON TRANSPORT / Membrane protein / bioenergetics / serial crystallography / lipidic cubic phase / flow-cell / sample delivery system
Function / homology
Function and homology information


cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / : / 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 / 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 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 / 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. / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / DINUCLEAR COPPER ION / HEME-AS / PROTOPORPHYRIN IX CONTAINING FE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Cytochrome c oxidase polypeptide 2A / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Thermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsGhosh, S. / Zoric, D. / Bjelcic, M. / Johannesson, J. / Sandelin, E. / Branden, G. / Neutze, R.
Funding support Sweden, European Union, 6items
OrganizationGrant numberCountry
Swedish Research Council2015-00560 Sweden
European Union (EU)789030European Union
European Union (EU)963936European Union
The Swedish Foundation for Strategic Research17-0060 Sweden
Swedish Research Council2017-06734 Sweden
Swedish Research Council2021-05662 Sweden
CitationJournal: J.Appl.Crystallogr. / Year: 2023
Title: A simple goniometer-compatible flow cell for serial synchrotron X-ray crystallography.
Authors: Ghosh, S. / Zoric, D. / Dahl, P. / Bjelcic, M. / Johannesson, J. / Sandelin, E. / Borjesson, P. / Bjorling, A. / Banacore, A. / Edlund, P. / Aurelius, O. / Milas, M. / Nan, J. / Shilova, A. ...Authors: Ghosh, S. / Zoric, D. / Dahl, P. / Bjelcic, M. / Johannesson, J. / Sandelin, E. / Borjesson, P. / Bjorling, A. / Banacore, A. / Edlund, P. / Aurelius, O. / Milas, M. / Nan, J. / Shilova, A. / Gonzalez, A. / Mueller, U. / Branden, G. / Neutze, R.
History
DepositionDec 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 29, 2024Group: Data collection / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity_src_gen / pdbx_validate_chiral
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)92,96722
Polymers85,8913
Non-polymers7,07619
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13830 Å2
ΔGint-155 kcal/mol
Surface area26030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.060, 100.170, 96.620
Angle α, β, γ (deg.)90.000, 126.760, 90.000
Int Tables number5
Space group name H-MC121

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


Mass: 63540.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: cbaA, TTHA1135 / Production host: Thermus thermophilus HB8 (bacteria) / References: UniProt: Q5SJ79, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 / Cytochrome c ba(3) subunit II / Cytochrome c oxidase polypeptide II / Cytochrome cba3 subunit 2


Mass: 18581.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: cbaB, ctaC, TTHA1134 / Production host: Thermus thermophilus HB8 (bacteria) / Strain (production host): HB8 / References: UniProt: Q5SJ80, cytochrome-c oxidase

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Protein/peptide , 1 types, 1 molecules C

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


Mass: 3769.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: cbaD, TTHA1133 / Production host: Thermus thermophilus HB8 (bacteria) / Strain (production host): HB8 / References: UniProt: P82543, cytochrome-c oxidase

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Non-polymers , 6 types, 123 molecules

#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 920.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H64FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C21H40O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


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


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.3 Å3/Da / Density % sol: 62.69 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 5.3
Details: 1.4 M NaCl, 100 mM MES pH 5.3 with 36 % to 39 % (v/v) PEG 400

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.12→25.802 Å / Num. obs: 65010 / % possible obs: 100 % / Redundancy: 123.6 % / CC1/2: 0.99 / Net I/σ(I): 6.8
Reflection shellResolution: 2.12→2.2 Å / Num. unique obs: 6268 / CC1/2: 0.52
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionDescription: Capillary-based flow-cell / Flow rate: 1.2 µL/min / Injector diameter: 200 µm / Injector temperature: 298 K

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→25.802 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.174 / WRfactor Rwork: 0.142 / SU B: 4.907 / SU ML: 0.119 / Average fsc free: 0.9029 / Average fsc work: 0.9055 / Cross valid method: FREE R-VALUE / ESU R: 0.141 / ESU R Free: 0.13
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1844 3207 5.076 %
Rwork0.152 59978 -
all0.154 --
obs-63185 99.932 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 48.819 Å2
Baniso -1Baniso -2Baniso -3
1-0.014 Å20 Å20.007 Å2
2---0.016 Å20 Å2
3----0.004 Å2
Refinement stepCycle: LAST / Resolution: 2.12→25.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5910 0 384 104 6398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136491
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166397
X-RAY DIFFRACTIONr_angle_refined_deg1.721.6618841
X-RAY DIFFRACTIONr_angle_other_deg1.2761.57514636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2625749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98520.608263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47315890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3841526
X-RAY DIFFRACTIONr_chiral_restr0.0830.2777
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027062
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021534
X-RAY DIFFRACTIONr_nbd_refined0.2210.21316
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.25442
X-RAY DIFFRACTIONr_nbtor_refined0.1740.23105
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22895
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2140
X-RAY DIFFRACTIONr_metal_ion_refined0.120.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2720.28
X-RAY DIFFRACTIONr_nbd_other0.1880.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2220.29
X-RAY DIFFRACTIONr_mcbond_it3.6644.6763005
X-RAY DIFFRACTIONr_mcbond_other3.6624.6753003
X-RAY DIFFRACTIONr_mcangle_it4.8617.0043751
X-RAY DIFFRACTIONr_mcangle_other4.8617.0043751
X-RAY DIFFRACTIONr_scbond_it4.6895.4393484
X-RAY DIFFRACTIONr_scbond_other4.6885.443485
X-RAY DIFFRACTIONr_scangle_it6.8867.8425089
X-RAY DIFFRACTIONr_scangle_other6.8857.8445090
X-RAY DIFFRACTIONr_lrange_it8.12855.1577229
X-RAY DIFFRACTIONr_lrange_other8.12855.1467219
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
2.12-2.1750.3262050.31244290.31246340.7010.7110.292
2.175-2.2340.2882480.28242250.28244730.7560.7610.26
2.234-2.2980.2711990.25742060.25844050.8270.8270.235
2.298-2.3680.2262040.22740550.22742590.870.8730.203
2.368-2.4450.2411870.21439810.21641680.8940.8880.184
2.445-2.530.2211840.19238360.19340200.8980.9140.165
2.53-2.6250.212030.16936260.17138290.9260.9340.143
2.625-2.7310.1941810.15535220.15737030.9360.9450.131
2.731-2.8510.2031870.14534200.14836070.9430.9540.125
2.851-2.9880.1751980.13931760.14133740.9510.9580.12
2.988-3.1470.1831920.13131000.13432920.9540.9620.118
3.147-3.3350.1711510.12629330.12930840.9630.9690.115
3.335-3.5610.1831460.11827580.12129040.9620.9730.11
3.561-3.840.1311780.10725220.10827000.9760.980.103
3.84-4.1980.151280.11223840.11425120.9670.9770.111
4.198-4.6780.1451480.12521270.12622750.970.9740.128
4.678-5.3720.185790.1419220.14220010.9620.9650.148
5.372-6.5090.155760.15116490.15117250.9650.9680.16
6.509-8.9260.162760.13212960.13313720.9730.9750.152
8.926-25.8020.286370.1768110.188480.9190.9570.208

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