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- PDB-1yg0: Solution structure of apo-CopP from Helicobacter pylori -

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Basic information

Entry
Database: PDB / ID: 1yg0
TitleSolution structure of apo-CopP from Helicobacter pylori
ComponentsCOP associated protein
KeywordsMETAL TRANSPORT / open-faced beta-sandwich / missing C-terminal beta-sheet
Function / homology
Function and homology information


copper ion transport / copper ion binding
Similarity search - Function
Copper ion binding protein / Heavy metal-associated domain, copper ion-binding / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits ...Copper ion binding protein / Heavy metal-associated domain, copper ion-binding / Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COP-associated protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model type detailsminimized average
AuthorsLee, B.J. / Park, S.J.
CitationJournal: To be published
Title: Solution structure of apo-CopP from Helicobacter pylori
Authors: Lee, B.J. / Park, S.J.
History
DepositionJan 4, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COP associated protein


Theoretical massNumber of molelcules
Total (without water)7,2031
Polymers7,2031
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein COP associated protein / HpCopP / Copper ion binding protein


Mass: 7203.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: copP / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: Q48271

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
141HNHA
NMR detailsText: This structure was determined using standard 2D and 3D techniques.

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Sample preparation

DetailsContents: 2mM HpCopP U-15N, 13C; 50mM phosphate buffer, 10mM DTT, 500mM NaCl NA; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 500mM NaCl, 10mM DTT / pH: 7 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Bruckerrefinement
CNS1.1Brungerstructure solution
NMRPipe5.4Delagliodata analysis
XWINNMR3.5Bruckercollection
X-PLOR3.8Bruckerrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
Details: The structures are based on a total of 1250 restraints, 1115 are NOE-derived distance constraints, 95 dihedral angle restraints, 40 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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