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- PDB-9vdj: Serial synchrotron crystallography structure of a ba3-type cytoch... -

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Basic information

Entry
Database: PDB / ID: 9vdj
TitleSerial synchrotron crystallography structure of a ba3-type cytochrome c oxidase using a goniometer-compatible chip-based platform
Components
  • (Cytochrome c oxidase subunit ...) x 2
  • Cytochrome c oxidase polypeptide 2A
KeywordsMEMBRANE PROTEIN / Proton-pump / Bioenergetics / complex IV / serial crystallography / lipidic cubic phase
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 / : / Cytochrome C oxidase subunit II, transmembrane domain superfamily / 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 subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKabbinale, A. / Branden, G. / Neutze, R. / Ghosh, S.
Funding supportEuropean Union, Sweden, 4items
OrganizationGrant numberCountry
European Research Council (ERC)789030 and 963936European Union
Swedish Research Council2017-06734, 2021-05662 and 2021-05981 Sweden
Swedish Research Council2015-00560 Sweden
The Swedish Foundation for Strategic ResearchID17-0060 Sweden
CitationJournal: J.Appl.Crystallogr. / Year: 2026
Title: A user-friendly goniometer-compatible fixed-target platform for macromolecular crystallography at synchrotrons
Authors: Ghosh, S. / Banacore, A. / Norder, P. / Bjelcic, M. / Kabbinale, A. / Nileshwar, P. / Wehlander, G. / de Sanctis, D. / Basu, S. / Orlans, J. / Vallejos, A. / Vallejos, L.M.G. / Neutze, R. / Branden, G.
History
DepositionJun 8, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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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)92,96722
Polymers85,8913
Non-polymers7,07619
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13930 Å2
ΔGint-154 kcal/mol
Surface area26270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.850, 100.320, 96.620
Angle α, β, γ (deg.)90.000, 126.760, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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 (strain ATCC 27634 / DSM 579 / HB8) (bacteria)
Gene: cbaA, TTHA1135 / Production host: Thermus thermophilus (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 (strain ATCC 27634 / DSM 579 / HB8) (bacteria)
Gene: cbaB, ctaC, TTHA1134 / Production host: Thermus thermophilus (bacteria) / 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 (strain ATCC 27634 / DSM 579 / HB8) (bacteria)
Gene: cbaD, TTHA1133 / Production host: Thermus thermophilus (bacteria) / References: UniProt: P82543, cytochrome-c oxidase

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Non-polymers , 6 types, 154 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.: 135 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.31 Å3/Da / Density % sol: 62.84 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / Details: 0.1M MES (pH 5.3), 1.4M NaCl, 39-41% PEG 400

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Data collection

DiffractionMean temperature: 293 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: Nov 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→37.2 Å / Num. obs: 49573 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 39.31 Å2 / CC1/2: 0.853 / Net I/σ(I): 3.07
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 4925 / CC1/2: 0.57
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
MxCuBEdata collection
CrystFELversion 9.0data reduction
PHASERphasing
PHENIX1.17.1_3660refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→32.15 Å / SU ML: 0.3242 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5082
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.264 2374 4.79 %
Rwork0.2091 47187 -
obs0.2118 49561 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.69 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6294 0 0 135 6429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00886491
X-RAY DIFFRACTIONf_angle_d1.2758841
X-RAY DIFFRACTIONf_chiral_restr0.0535969
X-RAY DIFFRACTIONf_plane_restr0.00671060
X-RAY DIFFRACTIONf_dihedral_angle_d23.95031067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.33431280.26472783X-RAY DIFFRACTION99.93
2.35-2.40.33171250.24912796X-RAY DIFFRACTION100
2.4-2.450.30671200.24952759X-RAY DIFFRACTION100
2.45-2.520.29531350.23742746X-RAY DIFFRACTION100
2.52-2.580.30741360.22982779X-RAY DIFFRACTION100
2.58-2.660.29851260.2322786X-RAY DIFFRACTION100
2.66-2.740.29171350.21582760X-RAY DIFFRACTION99.97
2.74-2.840.27261460.20942763X-RAY DIFFRACTION100
2.84-2.960.27661330.20752774X-RAY DIFFRACTION99.97
2.96-3.090.25281770.19522718X-RAY DIFFRACTION99.97
3.09-3.250.26321720.19632747X-RAY DIFFRACTION100
3.25-3.460.22581490.18652779X-RAY DIFFRACTION100
3.46-3.720.25041180.1822791X-RAY DIFFRACTION100
3.72-4.10.25421190.18192799X-RAY DIFFRACTION100
4.1-4.690.23651260.19622814X-RAY DIFFRACTION100
4.69-5.90.25071530.21132784X-RAY DIFFRACTION100
5.9-32.150.27571760.23882809X-RAY DIFFRACTION99.8
Refinement TLS params.Method: refined / Origin x: 3.26257304278 Å / Origin y: 1.70022564511 Å / Origin z: 26.386612537 Å
111213212223313233
T0.298260537764 Å2-0.0175591105999 Å2-0.00348209595504 Å2-0.262909393104 Å20.0441441611464 Å2--0.247508841946 Å2
L1.55179253948 °2-0.239374830948 °2-0.251292818395 °2-0.687475334933 °20.147386314196 °2--0.535486185299 °2
S0.0423611763592 Å °0.198459997144 Å °0.124587168885 Å °-0.0476556284973 Å °-0.0219492561495 Å °-0.133272606582 Å °0.00915460497138 Å °-0.00411784227503 Å °-0.0203451077891 Å °
Refinement TLS groupSelection details: all

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