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- PDB-9ilt: Crystal structure of alternative complex III from Chloroflexus au... -

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Basic information

Entry
Database: PDB / ID: 9ilt
TitleCrystal structure of alternative complex III from Chloroflexus aurantiacus
Components
  • (Quinol:cytochrome c oxidoreductase ...) x 2
  • ActG
  • Cytochrome c domain-containing protein
  • Cytochrome c7-like domain-containing protein
  • Fe-S-cluster-containing hydrogenase components 1-like protein
  • Polysulphide reductase NrfD
  • subunit I
KeywordsMEMBRANE PROTEIN / alternative complex III / Chloroflexus aurantiacus / photosynthetic electron transport chains / quinol: electron acceptor oxidoreductase
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
NrfD family / Alternative complex III, ActD subunit / MoCo/4Fe-4S cofactor protein extended Tat translocation domain / Polysulphide reductase, NrfD / Alternative complex III, ActD subunit / Cytochrome c7-like / Cytochrome c7 and related cytochrome c / Cytochrome C oxidase, cbb3-type, subunit III / Multiheme cytochrome superfamily / 4Fe-4S dicluster domain ...NrfD family / Alternative complex III, ActD subunit / MoCo/4Fe-4S cofactor protein extended Tat translocation domain / Polysulphide reductase, NrfD / Alternative complex III, ActD subunit / Cytochrome c7-like / Cytochrome c7 and related cytochrome c / Cytochrome C oxidase, cbb3-type, subunit III / Multiheme cytochrome superfamily / 4Fe-4S dicluster domain / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
FE3-S4 CLUSTER / HEME C / IRON/SULFUR CLUSTER / Cytochrome c7-like domain-containing protein / Fe-S-cluster-containing hydrogenase components 1-like protein / Polysulphide reductase NrfD / Quinol:cytochrome c oxidoreductase membrane protein / Cytochrome c domain-containing protein / Quinol:cytochrome c oxidoreductase quinone-binding subunit 2 / Uncharacterized protein
Similarity search - Component
Biological speciesChloroflexus aurantiacus J-10-fl (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsXu, X. / Wu, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870740, 32171227, 31570738, 32000034, 82101628 China
CitationJournal: Structure / Year: 2025
Title: Crystal structure of the alternative complex III from the phototrophic bacterium Chloroflexus aurantiacus.
Authors: Wu, W. / Fang, H. / He, H. / Wu, J. / Gong, Z. / Li, C. / Pei, X. / Xu, X.
History
DepositionJul 1, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c7-like domain-containing protein
B: Fe-S-cluster-containing hydrogenase components 1-like protein
C: Polysulphide reductase NrfD
D: Quinol:cytochrome c oxidoreductase membrane protein
E: Cytochrome c domain-containing protein
F: Quinol:cytochrome c oxidoreductase quinone-binding subunit 2
G: ActG
I: subunit I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,84318
Polymers298,7818
Non-polymers5,06210
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45190 Å2
ΔGint-448 kcal/mol
Surface area85790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.016, 153.063, 173.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 5 types, 5 molecules ABCEG

#1: Protein Cytochrome c7-like domain-containing protein


Mass: 25247.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WEV2
#2: Protein Fe-S-cluster-containing hydrogenase components 1-like protein


Mass: 113115.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WEV3
#3: Protein Polysulphide reductase NrfD


Mass: 55223.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WEV4
#5: Protein Cytochrome c domain-containing protein


Mass: 23017.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WEV6
#7: Protein ActG


Mass: 12485.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WEV8

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Quinol:cytochrome c oxidoreductase ... , 2 types, 2 molecules DF

#4: Protein Quinol:cytochrome c oxidoreductase membrane protein


Mass: 19648.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WEV5
#6: Protein Quinol:cytochrome c oxidoreductase quinone-binding subunit 2


Mass: 45721.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
References: UniProt: A9WEV7

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Protein/peptide , 1 types, 1 molecules I

#8: Protein/peptide subunit I


Mass: 4322.134 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)

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Non-polymers , 3 types, 10 molecules

#9: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#10: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#11: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 100 mM glycine at pH 9.0 and 26% (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.25→40.3 Å / Num. obs: 57488 / % possible obs: 89.82 % / Redundancy: 6.7 % / CC1/2: 0.996 / Net I/σ(I): 10.44
Reflection shellResolution: 3.25→3.366 Å / Num. unique obs: 5927 / CC1/2: 0.748

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158)refinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8K9F

8k9f


Resolution: 3.25→40.3 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2858 2651 4.91 %
Rwork0.249 --
obs0.2507 54042 89.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→40.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19379 0 289 0 19668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00320277
X-RAY DIFFRACTIONf_angle_d0.92127777
X-RAY DIFFRACTIONf_dihedral_angle_d6.8942749
X-RAY DIFFRACTIONf_chiral_restr0.0683034
X-RAY DIFFRACTIONf_plane_restr0.0043513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.310.42151490.36882990X-RAY DIFFRACTION100
3.31-3.370.41541260.34982964X-RAY DIFFRACTION100
3.37-3.430.36931280.3412304X-RAY DIFFRACTION89
3.48-3.520.3608730.33871278X-RAY DIFFRACTION82
3.52-3.60.3551600.32422963X-RAY DIFFRACTION100
3.6-3.660.33171030.32241950X-RAY DIFFRACTION90
3.7-3.790.33941020.31082190X-RAY DIFFRACTION88
3.79-3.890.31151250.28822628X-RAY DIFFRACTION94
3.94-4.020.3468930.29991835X-RAY DIFFRACTION92
4.02-4.170.32341690.26772978X-RAY DIFFRACTION100
4.17-4.340.29431550.25462977X-RAY DIFFRACTION100
4.34-4.530.28751710.23152984X-RAY DIFFRACTION100
4.53-4.770.26021630.22562993X-RAY DIFFRACTION100
4.77-5.070.26341610.21963006X-RAY DIFFRACTION100
5.07-5.460.26721680.21983018X-RAY DIFFRACTION100
5.46-6.010.27651540.23523030X-RAY DIFFRACTION100
6.01-6.870.26271460.23173050X-RAY DIFFRACTION100
6.87-8.650.23371610.21223088X-RAY DIFFRACTION100
8-100.23821440.21593165X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -37.1225 Å / Origin y: -35.2494 Å / Origin z: 41.8978 Å
111213212223313233
T0.2531 Å20.1076 Å2-0.007 Å2-0.3972 Å2-0.0459 Å2--0.3868 Å2
L0.2004 °2-0.193 °2-0.1273 °2-0.4421 °20.1227 °2--0.6057 °2
S-0.0195 Å °-0.0156 Å °0.0298 Å °-0.0563 Å °-0.0494 Å °0.0157 Å °-0.0762 Å °-0.1986 Å °-0.0007 Å °
Refinement TLS groupSelection details: all

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