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- PDB-6ptt: Soluble model of Arabidopsis thaliana CuA (Tt3LAt) -

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Basic information

Entry
Database: PDB / ID: 6ptt
TitleSoluble model of Arabidopsis thaliana CuA (Tt3LAt)
ComponentsCytochrome c oxidase subunit 2
KeywordsELECTRON TRANSPORT / OXIDOREDUCTASE / CuA site / electron transfer / cupredoxin fold
Function / homology
Function and homology information


cytochrome-c oxidase / cytochrome-c oxidase activity / respirasome / copper ion binding / plasma membrane
Similarity search - Function
Cytochrome C oxidase subunit IIa, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane / Ba3-like heme-copper oxidase subunit II, C-terminal / 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 ...Cytochrome C oxidase subunit IIa, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane / Ba3-like heme-copper oxidase subunit II, C-terminal / 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
DINUCLEAR COPPER ION / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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: Chem.Commun.(Camb.) / Year: 2020
Title: Unexpected electron spin density on the axial methionine ligand in CuAsuggests its involvement in electron pathways.
Authors: Morgada, M.N. / Llases, M.E. / Giannini, E. / Castro, M.A. / Alzari, P.M. / Murgida, D.H. / Lisa, M.N. / Vila, A.J.
History
DepositionJul 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 3, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c oxidase subunit 2
B: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3984
Polymers28,1442
Non-polymers2542
Water4,504250
1
A: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1992
Polymers14,0721
Non-polymers1271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1992
Polymers14,0721
Non-polymers1271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.335, 73.734, 79.135
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUVALVAL(chain 'A' and (resid 50 through 58 or resid 60 through 168))AA50 - 588 - 16
12GLNGLNGLUGLU(chain 'A' and (resid 50 through 58 or resid 60 through 168))AA60 - 16818 - 126
21LEULEUVALVAL(chain 'B' and (resid 50 through 58 or resid 60 through 168))BB50 - 588 - 16
22GLNGLNGLUGLU(chain 'B' and (resid 50 through 58 or resid 60 through 168))BB60 - 16818 - 126

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Components

#1: Protein Cytochrome c oxidase subunit 2 / Cytochrome c ba(3) subunit II / Cytochrome c oxidase polypeptide II / Cytochrome cba3 subunit 2


Mass: 14071.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: cbaB, ctaC / Production host: Escherichia coli (E. coli)
References: UniProt: P98052, UniProt: Q5SJ80*PLUS, cytochrome-c oxidase
#2: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 100 mM Hepes, 1.5 M LiSO4, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.3679 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3679 Å / Relative weight: 1
ReflectionResolution: 1.84→43.07 Å / Num. obs: 26102 / % possible obs: 98.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 22.74 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.043 / Rrim(I) all: 0.089 / Net I/σ(I): 16.1
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 3 / Num. unique obs: 1572 / CC1/2: 0.896 / Rpim(I) all: 0.254 / Rrim(I) all: 0.508 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.14rc3_3199refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CUA

2cua


Resolution: 1.84→43.07 Å / SU ML: 0.2306 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 21.4926
RfactorNum. reflection% reflection
Rfree0.2137 1372 5.26 %
Rwork0.1697 --
obs0.1719 26059 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 27.75 Å2
Refinement stepCycle: LAST / Resolution: 1.84→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 4 250 2142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01971953
X-RAY DIFFRACTIONf_angle_d1.1932673
X-RAY DIFFRACTIONf_chiral_restr0.1085297
X-RAY DIFFRACTIONf_plane_restr0.0092350
X-RAY DIFFRACTIONf_dihedral_angle_d14.02051143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.910.37181660.37432390X-RAY DIFFRACTION98.69
1.91-1.980.30611650.25922424X-RAY DIFFRACTION98.55
1.98-2.070.22581150.17712469X-RAY DIFFRACTION98.55
2.07-2.180.20181140.15832517X-RAY DIFFRACTION99.47
2.18-2.320.19821450.14972482X-RAY DIFFRACTION99.06
2.32-2.50.20971570.16152448X-RAY DIFFRACTION97.79
2.5-2.750.22291280.16312475X-RAY DIFFRACTION98.34
2.75-3.150.24431330.16662492X-RAY DIFFRACTION97.8
3.15-3.960.18261300.15182478X-RAY DIFFRACTION95.6
3.96-43.070.17771190.16362512X-RAY DIFFRACTION92.61
Refinement TLS params.Method: refined / Origin x: 24.8558967244 Å / Origin y: 6.40112084807 Å / Origin z: 23.4375790861 Å
111213212223313233
T0.110991217486 Å2-0.00628520611247 Å20.00151419051522 Å2-0.0884596699915 Å2-0.00464328397273 Å2--0.172657022942 Å2
L0.594252438358 °2-0.265776729162 °21.0804557742 °2-0.449810504337 °2-0.682073698288 °2--3.35288166363 °2
S-0.0210467495262 Å °-0.0268526097825 Å °0.0573330544481 Å °0.0390141478201 Å °0.0128822383417 Å °0.00688340100816 Å °-0.109931670359 Å °-0.0381137705237 Å °0.0133613047206 Å °
Refinement TLS groupSelection details: all

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