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- PDB-3omn: Catalytic core subunits (I and II) of cytochrome C oxidase from R... -

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Basic information

Entry
Database: PDB / ID: 3omn
TitleCatalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides with D132A mutation in the reduced state
Components(Cytochrome c ...) x 2
KeywordsOXIDOREDUCTASE / TRANSMEMBRANE PROTEIN COMPLEX
Function / homology
Function and homology information


respiratory chain complex IV / cytochrome-c oxidase / oxidative phosphorylation / electron transport coupled proton transport / cytochrome-c oxidase activity / respirasome / copper ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome c oxidase, subunit I bacterial type / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II ...Cytochrome c oxidase, subunit I bacterial type / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / 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. / Cupredoxins - blue copper proteins / Cupredoxin / Helix Hairpins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / COPPER (I) ION / HEME-A / (2S,3R)-heptane-1,2,3-triol / HYDROXIDE ION / TRIDECANE / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesRhodobacter sphaeroides 2.4.1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLiu, J. / Qin, L. / Ferguson-Miller, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump.
Authors: Liu, J. / Qin, L. / Ferguson-Miller, S.
History
DepositionAug 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 2, 2012Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c oxidase, aa3 type, subunit I
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase, aa3 type, subunit I
D: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,82047
Polymers176,2284
Non-polymers11,59243
Water8,287460
1
A: Cytochrome c oxidase, aa3 type, subunit I
B: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,50226
Polymers88,1142
Non-polymers6,38824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17840 Å2
ΔGint-187 kcal/mol
Surface area26210 Å2
MethodPISA
2
C: Cytochrome c oxidase, aa3 type, subunit I
D: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,31821
Polymers88,1142
Non-polymers5,20419
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15840 Å2
ΔGint-183 kcal/mol
Surface area26580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.670, 132.033, 176.286
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Cytochrome c ... , 2 types, 4 molecules ACBD

#1: Protein Cytochrome c oxidase, aa3 type, subunit I /


Mass: 59496.344 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 17-551 / Mutation: D132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria)
Strain: ATCC 17023/2.4.1/NCIB 8253/DSM 158 / Gene: coxI, CTAD, RHOS4_04590, RSP_1877 / Plasmid: pRK415-1 / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): Rhodobacter sphaeroides / References: UniProt: Q3J5A7, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 /


Mass: 28617.637 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 30-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria)
Strain: ATCC 17023/2.4.1/NCIB 8253/DSM 158 / Gene: coxII, CTAB, CTAC, RHOS4_04060, RSP_1826 / Plasmid: pRK415-1 / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): Rhodobacter sphaeroides / References: UniProt: Q3J5G0, cytochrome-c oxidase

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Sugars , 1 types, 11 molecules

#4: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 10 types, 492 molecules

#3: Chemical ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#5: Chemical
ChemComp-TRD / TRIDECANE / LIPID FRAGMENT / Tridecane


Mass: 184.361 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C13H28
#6: Chemical
ChemComp-HEA / HEME-A / Heme A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#7: Chemical
ChemComp-CU1 / COPPER (I) ION / Copper


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-HTH / (2S,3R)-heptane-1,2,3-triol / heptane-1,2,3-triol


Mass: 148.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O3
#12: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsLIGANDS LABELLED AS TRD ARE ALL ALKYL CHAINS WITH DIFFERENT LENGTHS OF EITHER DMU OR NATIVE ...LIGANDS LABELLED AS TRD ARE ALL ALKYL CHAINS WITH DIFFERENT LENGTHS OF EITHER DMU OR NATIVE MEMBRANE LIPIDS SUCH AS PHOSPHATIDYL ETHANOLAMINE OR CARDIOLIPIN. THE AUTHORS DO NOT KNOW FOR SURE THE IDENTITIES OF THE COMPLETE MOLECULES.

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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: 4.12 Å3/Da / Density % sol: 70.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 26-29% PEG-400, pH 6.3, VAPOR DIFFUSION, SITTING DROP, reduced by dithionite, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 2, 2009
RadiationMonochromator: Diamond / Protocol: SINGLE WEAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 153760 / % possible obs: 97.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.086 / Χ2: 1.025 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.235.10.575131301.004184
2.23-2.325.90.479145231.023193.3
2.32-2.426.60.391153651.044198.4
2.42-2.557.20.301156391.0391100
2.55-2.717.60.216157061.0371100
2.71-2.927.60.153156991.051100
2.92-3.217.60.116157271.0121100
3.21-3.687.60.093158140.9781100
3.68-4.637.50.064158871.0471100
4.63-507.30.048162701.013199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→42.7 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2189 / WRfactor Rwork: 0.1978 / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8539 / SU B: 3.878 / SU ML: 0.103 / SU R Cruickshank DPI: 0.166 / SU Rfree: 0.1459 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 4627 3 %RANDOM
Rwork0.1978 ---
obs0.1985 153587 97.19 %-
all-153587 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.01 Å2 / Biso mean: 43.9531 Å2 / Biso min: 8.39 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å20 Å20 Å2
2---0.31 Å20 Å2
3---2.16 Å2
Refinement stepCycle: LAST / Resolution: 2.15→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12339 0 645 460 13444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02213747
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.98518773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.59451606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.0422.749513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.643151861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0541537
X-RAY DIFFRACTIONr_chiral_restr0.0860.22055
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210370
X-RAY DIFFRACTIONr_nbd_refined0.2090.27247
X-RAY DIFFRACTIONr_nbtor_refined0.3110.29465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2679
X-RAY DIFFRACTIONr_metal_ion_refined0.1020.222
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0250.23
X-RAY DIFFRACTIONr_mcbond_it0.5741.58181
X-RAY DIFFRACTIONr_mcangle_it0.953212845
X-RAY DIFFRACTIONr_scbond_it1.23736575
X-RAY DIFFRACTIONr_scangle_it1.7564.55924
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 266 -
Rwork0.259 8708 -
all-8974 -
obs--77.71 %

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