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- PDB-6pcf: Human Coa6: W59C mutant protein -

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Basic information

Entry
Database: PDB / ID: 6pcf
TitleHuman Coa6: W59C mutant protein
ComponentsCytochrome c oxidase assembly factor 6 homolog
KeywordsMETAL BINDING PROTEIN / Coa6 copper Cytochrome c oxidase mitochondria structure
Function / homology
Function and homology information


mitochondrial respiratory chain complex IV assembly / respiratory chain complex IV assembly / Mitochondrial protein import / mitochondrial intermembrane space / copper ion binding / mitochondrion / RNA binding / nucleoplasm
Similarity search - Function
Cytochrome c oxidase assembly factor 6 homolog / : / Cytochrome c oxidase, subunit VIb superfamily / Cytochrome oxidase c subunit VIb / Coiled coil-helix-coiled coil-helix (CHCH) domain profile.
Similarity search - Domain/homology
Cytochrome c oxidase assembly factor 6 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMaher, M.J. / Maghool, S.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP140102746 Australia
National Health and Medical Research Council (NHMRC, Australia)GNT1165217 Australia
National Health and Medical Research Council (NHMRC, Australia)GNT1140851 Australia
CitationJournal: Life Sci Alliance / Year: 2019
Title: Structural and functional characterization of the mitochondrial complex IV assembly factor Coa6.
Authors: Maghool, S. / Cooray, N.D.G. / Stroud, D.A. / Aragao, D. / Ryan, M.T. / Maher, M.J.
History
DepositionJun 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Cytochrome c oxidase assembly factor 6 homolog
C: Cytochrome c oxidase assembly factor 6 homolog
A: Cytochrome c oxidase assembly factor 6 homolog
D: Cytochrome c oxidase assembly factor 6 homolog


Theoretical massNumber of molelcules
Total (without water)31,5724
Polymers31,5724
Non-polymers00
Water45025
1
A: Cytochrome c oxidase assembly factor 6 homolog
D: Cytochrome c oxidase assembly factor 6 homolog

B: Cytochrome c oxidase assembly factor 6 homolog
C: Cytochrome c oxidase assembly factor 6 homolog


Theoretical massNumber of molelcules
Total (without water)31,5724
Polymers31,5724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area2750 Å2
ΔGint-16 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.386, 47.823, 48.114
Angle α, β, γ (deg.)116.86, 98.68, 104.26
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cytochrome c oxidase assembly factor 6 homolog


Mass: 7892.980 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COA6, C1orf31 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JTJ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris, pH 5.7, 0.23 M MgCl2.6H2O, 29% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 15400 / % possible obs: 98.4 % / Redundancy: 3.2 % / Net I/σ(I): 14.4
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 1521

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0238refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PCE

6pce


Resolution: 2.2→38.25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 15.351 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.254 / ESU R Free: 0.205 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 713 4.6 %RANDOM
Rwork0.20073 ---
obs0.20273 14685 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 67.389 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-1.39 Å2-0.6 Å2
2--0.25 Å20.13 Å2
3---0.29 Å2
Refinement stepCycle: 1 / Resolution: 2.2→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 0 25 2064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132095
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181844
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.6562802
X-RAY DIFFRACTIONr_angle_other_deg1.171.6044300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3255239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22421.94134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65215398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1541518
X-RAY DIFFRACTIONr_chiral_restr0.0530.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022322
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02500
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.6345.764968
X-RAY DIFFRACTIONr_mcbond_other8.6275.763967
X-RAY DIFFRACTIONr_mcangle_it10.0358.6421203
X-RAY DIFFRACTIONr_mcangle_other10.0358.6441204
X-RAY DIFFRACTIONr_scbond_it11.1246.4381127
X-RAY DIFFRACTIONr_scbond_other11.1196.441128
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.3889.3421600
X-RAY DIFFRACTIONr_long_range_B_refined14.25265.1572410
X-RAY DIFFRACTIONr_long_range_B_other14.2565.1472410
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.178→2.235 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 45 -
Rwork0.273 831 -
obs--77.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6470.02950.62391.67640.32280.71450.0926-0.11940.01950.004-0.01080.09870.1681-0.0945-0.08180.121-0.0189-0.05860.0298-0.03230.151-12.166222.972712.0143
21.05430.73680.88851.9694-0.25531.28180.05430.1472-0.10240.08670.0579-0.07490.02780.1648-0.11230.03530.0302-0.0120.0912-0.08550.09621.069632.71816.7437
32.3791-0.9230.88380.7395-0.06860.53640.15720.2158-0.0376-0.0817-0.1093-0.00660.01230.0667-0.04790.11180.01550.03920.0628-0.03960.054-3.39917.5572-2.3773
41.5571-0.74510.55930.7568-0.34991.19960.33550.06010.27190.0294-0.18870.0116-0.05730.2583-0.14680.1837-0.09140.15670.1073-0.08990.14412.349314.4967-2.3862
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B49 - 113
2X-RAY DIFFRACTION2C56 - 111
3X-RAY DIFFRACTION3A56 - 113
4X-RAY DIFFRACTION4D50 - 113

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