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- PDB-6tpb: NMR structure of the apo-form of Pseudomonas fluorescens CopC -

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Basic information

Entry
Database: PDB / ID: 6tpb
TitleNMR structure of the apo-form of Pseudomonas fluorescens CopC
ComponentsPutative copper resistance protein
KeywordsCHAPERONE / periplasmic / Copper binding / histidine brace
Function / homology
Function and homology information


copper ion transport / response to copper ion / periplasmic space / copper ion binding / plasma membrane
Similarity search - Function
Copper transport protein C/D / : / CopC domain / CopC domain / Copper resistance protein CopC/internalin, immunoglobulin-like / Immunoglobulin E-set
Similarity search - Domain/homology
Copper resistance protein C
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsPersson, K.C. / Mayzel, M. / Karlsson, B.G. / Peciulyte, A. / Olsson, L. / Wittung Stafshede, P. / Salomon Johansen, K. / Horvath, I.
Funding support Denmark, 1items
OrganizationGrant numberCountry
European Commission608473 Denmark
CitationJournal: To Be Published
Title: NMR structure of Pseudomonas fluorescens CopC
Authors: Persson, K.C. / Mayzel, M. / Karlsson, B.G. / Peciulyte, A. / Olsson, L. / Wittung Stafshede, P. / Salomon Johansen, K. / Horvath, I.
History
DepositionDec 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative copper resistance protein


Theoretical massNumber of molelcules
Total (without water)10,1101
Polymers10,1101
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5730 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2020
RepresentativeModel #1target function

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Components

#1: Protein Putative copper resistance protein


Mass: 10110.294 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: PFLU_3946 / Production host: Escherichia coli (E. coli) / References: UniProt: C3JYL7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HN(CA)CO
161isotropic13D HNCA
1101isotropic13D HN(CO)CA
191isotropic13D HN(CA)CB
181isotropic13D HN(COCA)CB
171isotropic13D 1H-15N NOESY
1141isotropic13D H(CCO)NH
1131isotropic13D C(CO)NH
1121isotropic13D 1H-13C NOESY aliphatic
1111isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.7 mM [U-100% 13C; U-100% 15N] CopC, 90% H2O/10% D2O
Label: Sample 1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.7 mM / Component: CopC / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsDetails: 40mM MES, 150mM NaCl / Ionic strength: 150 mM / Label: Buffer / pH: 5.6 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98Guntert, Mumenthaler and Wuthrichstructure calculation
CYANA3.98Guntert, Mumenthaler and Wuthrichchemical shift assignment
WHAT IFVriendrefinement
CcpNmr AnalysisCCPNdata analysis
RefinementMethod: molecular dynamics / Software ordinal: 3 / Details: The program Yasara was used
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: 20 / Conformers calculated total number: 20 / Conformers submitted total number: 20

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