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- PDB-2k6z: Solution structures of copper loaded form PCuA (trans conformatio... -

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Basic information

Entry
Database: PDB / ID: 2k6z
TitleSolution structures of copper loaded form PCuA (trans conformation of the peptide bond involving the nitrogen of P14)
ComponentsPutative uncharacterized protein TTHA1943
KeywordsMETAL TRANSPORT / PCuA / copper transfer protein
Function / homologyPCu(A)C copper chaperone / Copper chaperone PCuAC / Copper chaperone PCuAC superfamily / Copper chaperone PCu(A)C / Immunoglobulin-like / Sandwich / Mainly Beta / COPPER (I) ION / Transporter
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsAbriata, L.A. / Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Gkazonis, P.A. / Spyroulias, G.A. / Vila, A.J. / Wang, S.
CitationJournal: Nat.Chem.Biol. / Year: 2008
Title: Mechanism of Cu(A) assembly.
Authors: Abriata, L.A. / Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Gkazonis, P. / Spyroulias, G.A. / Vila, A.J. / Wang, S.
History
DepositionJul 28, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein TTHA1943
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2862
Polymers13,2231
Non-polymers641
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)31 / 31structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Putative uncharacterized protein TTHA1943


Mass: 13222.550 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1943 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SGY7
#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1323D CBCA(CO)NH
1423D HNCO
1523D HNCA
1623D HN(CA)CB
1723D (H)CCH-TOCSY
1823D HBHA(CO)NH
1913D 1H-15N NOESY
11023D 1H-13C NOESY
11112D 1H-1H NOESY
112115N R1
113115N R2
11411H-15N NOE

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMentity_1[U-100% 15N]1
0.8 mMentity_1[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 50mM Pi / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE5002
Bruker AvanceBrukerAVANCE4003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospindata analysis
CARAKeller, R. et al.chemical shift assignment
CARAKeller, R. et al.peak picking
CYANAGuntert, P. et al.structure solution
AmberCase, D. et al.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1701 / Protein phi angle constraints total count: 61 / Protein psi angle constraints total count: 62
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 31 / Conformers submitted total number: 31

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