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- PDB-4w9z: Crystal structure of the periplasmic domain of subunit II of cyto... -

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Basic information

Entry
Database: PDB / ID: 4w9z
TitleCrystal structure of the periplasmic domain of subunit II of cytochrome oxidase (CoxB) of Bradyrhizobium japonicum
ComponentsCytochrome c oxidase subunit 2
KeywordsOXIDOREDUCTASE / CuA / Respiration
Function / homology
Function and homology information


cytochrome-c oxidase / cytochrome-c oxidase activity / ATP synthesis coupled electron transport / respirasome / copper ion binding / plasma membrane
Similarity search - Function
Cytochrome c oxidase subunit 2, C-terminal / 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 II, periplasmic domain ...Cytochrome c oxidase subunit 2, C-terminal / 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 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsQuade, N. / Abicht, H.K. / Hennecke, H. / Glockshuber, R.
CitationJournal: To Be Published
Title: Crystal structure of the periplasmic domain of subunit II of cytochrome oxidase (CoxB) of Bradyrhizobium japonicum
Authors: Quade, N. / Abicht, H.K. / Hennecke, H. / Glockshuber, R.
History
DepositionAug 28, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7253
Polymers15,5981
Non-polymers1272
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.431, 38.612, 59.644
Angle α, β, γ (deg.)90.000, 97.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome c oxidase subunit 2 /


Mass: 15598.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium diazoefficiens (bacteria)
Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110 / Gene: coxB, blr1170 / Plasmid: pET11a-CoxBPD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H7C6E5, cytochrome-c oxidase
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Potassium bromide, 0.1M Tris pH 7.5, 10% PEG1000, 10% PEG8000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 1.3 Å / Num. obs: 35883 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.269 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.053 / Χ2: 1.018 / Net I/σ(I): 20.13 / Num. measured all: 231266
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.3-1.330.960.2475.2515490266526520.27299.5
1.33-1.370.970.2315.7215305256925540.25499.4
1.37-1.410.9770.1956.8615360253225070.21499
1.41-1.450.9830.1697.7214160243623930.18698.2
1.45-1.50.9840.1598.9114787236123430.17499.2
1.5-1.550.9890.13510.8414918231323070.14699.7
1.55-1.610.9910.11712.8514529223722330.12899.8
1.61-1.680.9940.09914.8113561212721080.10899.1
1.68-1.750.9950.08317.7713037204520040.09198
1.75-1.840.9960.07721.1413560195819550.08399.8
1.84-1.940.9970.06623.9312914188818850.07299.8
1.94-2.060.9980.05428.5811749175417460.05999.5
2.06-2.20.9980.05130.8410476166916380.05598.1
2.2-2.370.9990.04635.8110960154415410.0599.8
2.37-2.60.9990.04337.779976143014280.04799.9
2.6-2.910.9990.03940.328656130212930.04299.3
2.91-3.360.9990.03146.627302115211350.03398.5
3.36-4.110.9990.02753.2466979749720.0399.8
4.11-5.810.9990.02753.7849677687520.02997.9
5.810.9990.03353.2328624424370.03598.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.19 Å38.61 Å
Translation1.19 Å38.61 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Cootmodel building
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHASERphasing
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TXV

4txv


Resolution: 1.3→59.12 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.1376 / WRfactor Rwork: 0.1131 / FOM work R set: 0.9419 / SU B: 0.955 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0364 / SU Rfree: 0.0356 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1336 1795 5 %RANDOM
Rwork0.1089 34089 --
obs0.1102 34089 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 169.86 Å2 / Biso mean: 16.637 Å2 / Biso min: 4.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-0.08 Å2
2--0.46 Å20 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 1.3→59.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1091 0 2 256 1349
Biso mean--8.39 30.95 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.021155
X-RAY DIFFRACTIONr_bond_other_d0.0010.021117
X-RAY DIFFRACTIONr_angle_refined_deg2.271.941570
X-RAY DIFFRACTIONr_angle_other_deg1.23832586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8125148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29424.650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50815203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.59154
X-RAY DIFFRACTIONr_chiral_restr0.1310.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211296
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02264
X-RAY DIFFRACTIONr_mcbond_it2.4571.11563
X-RAY DIFFRACTIONr_mcbond_other2.4091.103562
X-RAY DIFFRACTIONr_mcangle_it3.2191.673704
X-RAY DIFFRACTIONr_rigid_bond_restr6.32732272
X-RAY DIFFRACTIONr_sphericity_free37.673546
X-RAY DIFFRACTIONr_sphericity_bonded15.05452449
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.133 133 -
Rwork0.121 2512 -
all-2645 -
obs--99.44 %

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