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- PDB-6n5u: Crystal structure of Arabidopsis thaliana ScoI with copper bound -

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Basic information

Entry
Database: PDB / ID: 6n5u
TitleCrystal structure of Arabidopsis thaliana ScoI with copper bound
ComponentsProtein SCO1 homolog 1, mitochondrial
KeywordsMETAL BINDING PROTEIN / thioredoxin fold / metal ion / reduced form / metallochaperone / HCC1
Function / homology
Function and homology information


mitochondrial cytochrome c oxidase assembly / embryo development ending in seed dormancy / mitochondrial inner membrane / copper ion binding / mitochondrion
Similarity search - Function
Copper chaperone SCO1/SenC / SCO1/SenC / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (I) ION / Protein SCO1 homolog 1, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsLisa, M.N. / Giannini, E. / Llases, M.E. / Alzari, P.M. / Vila, A.J.
Funding support Argentina, 1items
OrganizationGrant numberCountry
National Research Council (NRC, Argentina)PICT-2012-1285 Argentina
CitationJournal: Febs J. / Year: 2020
Title: Arabidopsis thaliana Hcc1 is a Sco-like metallochaperone for CuAassembly in Cytochrome c Oxidase.
Authors: Llases, M.E. / Lisa, M.N. / Morgada, M.N. / Giannini, E. / Alzari, P.M. / Vila, A.J.
History
DepositionNov 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.4Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein SCO1 homolog 1, mitochondrial
B: Protein SCO1 homolog 1, mitochondrial
C: Protein SCO1 homolog 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4576
Polymers58,2673
Non-polymers1913
Water1,62190
1
A: Protein SCO1 homolog 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4862
Polymers19,4221
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein SCO1 homolog 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4862
Polymers19,4221
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein SCO1 homolog 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4862
Polymers19,4221
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.650, 80.440, 72.310
Angle α, β, γ (deg.)90.00, 94.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein SCO1 homolog 1, mitochondrial / Homolog of the copper chaperone SCO1 member 1 / HCC1


Mass: 19422.207 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HCC1, SCO1-1, At3g08950, T16O11.9 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 Star / References: UniProt: Q8VYP0
#2: Chemical ChemComp-CU1 / COPPER (I) ION


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


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100 mM Hepes pH 7.5, 23 % w/v PEG 3350, 10 % v/v Tacsimate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.66→44.75 Å / Num. obs: 17555 / % possible obs: 99 % / Redundancy: 2.9 % / Biso Wilson estimate: 49.62 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.05 / Rrim(I) all: 0.085 / Net I/σ(I): 5.7
Reflection shellResolution: 2.66→2.79 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2355 / CC1/2: 0.932 / Rpim(I) all: 0.24 / Rrim(I) all: 0.408 / % possible all: 99.6

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GGT

2ggt


Resolution: 2.66→44.75 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.872 / SU R Cruickshank DPI: 0.753 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.682 / SU Rfree Blow DPI: 0.287 / SU Rfree Cruickshank DPI: 0.295
RfactorNum. reflection% reflectionSelection details
Rfree0.233 866 4.94 %RANDOM
Rwork0.187 ---
obs0.19 17534 98.8 %-
Displacement parametersBiso mean: 54.98 Å2
Baniso -1Baniso -2Baniso -3
1--24.8352 Å20 Å213.2413 Å2
2--14.3536 Å20 Å2
3---10.4816 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: 1 / Resolution: 2.66→44.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3859 0 3 90 3952
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013948HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.145339HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1381SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes658HARMONIC5
X-RAY DIFFRACTIONt_it3948HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion16.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion506SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance9HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4492SEMIHARMONIC4
LS refinement shellResolution: 2.66→2.82 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2884 136 4.78 %
Rwork0.2259 2712 -
all0.229 2848 -
obs--99.58 %
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)
11.94-1.17831.65545.1872-0.66223.59780.06070.16890.10480.5232-0.2577-0.4905-0.20370.32430.19710.1777-0.0357-0.2045-0.32320.0335-0.139113.78849.824114.1764
21.6872-0.2088-0.1162.7230.1462.7617-0.04350.0168-0.0990.341-0.0267-0.29130.00840.02360.07020.20570.0261-0.214-0.3135-0.0255-0.101410.1865-16.997325.9665
31.6788-0.42950.55272.3764-0.17353.49630.2106-0.03510.0322-0.5152-0.05040.07040.5101-0.0522-0.16020.2974-0.0117-0.1595-0.31990.0066-0.1177-2.3154-3.6359-17.1037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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