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- PDB-1ybj: Structural and Dynamics studies of both apo and holo forms of the... -

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Basic information

Entry
Database: PDB / ID: 1ybj
TitleStructural and Dynamics studies of both apo and holo forms of the hemophore HasA
ComponentsHemophore HasA
KeywordsMETAL BINDING PROTEIN / alpha+beta structure / curved anti-parallel beta-sheet
Function / homology
Function and homology information


extracellular region / metal ion binding
Similarity search - Function
Heme-binding Protein A; Chain: A; / Haem-binding HasA / Haem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSerratia marcescens (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsWolff, N. / Izadi-Pruneyre, N. / Couprie, J. / Habeck, M. / Linge, J. / Rieping, W. / Wandersman, C. / Nilges, M. / Delepierre, M. / Lecroisey, A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Comparative analysis of structural and dynamic properties of the loaded and unloaded hemophore HasA: functional implications.
Authors: Wolff, N. / Izadi-Pruneyre, N. / Couprie, J. / Habeck, M. / Linge, J. / Rieping, W. / Wandersman, C. / Nilges, M. / Delepierre, M. / Lecroisey, A.
History
DepositionDec 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemophore HasA


Theoretical massNumber of molelcules
Total (without water)18,2891
Polymers18,2891
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)10 / 20structures with the lowest energy
RepresentativeModel #10lowest energy

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Components

#1: Protein Hemophore HasA / Heme acquisition system protein A


Mass: 18289.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: hasA / Plasmid: pSYC150 / Production host: Escherichia coli (E. coli) / Strain (production host): pop3 / References: UniProt: Q54450

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNHA
1223D 15N-separated NOESY
1323D 13C-separated NOESY
NMR detailsText: H-bond constraints according to the amide proton-deuterium exchange measurements (15N HSQC experiments)

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Sample preparation

Details
Solution-IDContentsSolvent system
11.8mM HasA 15N20mM sodium phosphate buffer, pH5.6; 90% H2O/10% D20
21.9mM HasA 15N,13C20mM sodium phosphate buffer, pH5.6; 90% H2O/10% D20
Sample conditionsIonic strength: 20mM sodium phosphate buffer / pH: 5.6 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1ccollection
NMRPipeF. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
XEASY1.3.13Bartels, C., Xia, T.H., Billeter, M., Guntert, P., Wuthrich, K.data analysis
ARIA/CNS2.0alphaLinge, J., Nilges, M., Habeck, M., Rieping, W.structure solution
ARIA/CNS2.0alphaLinge, J., Nilges, M., Habeck, M., Rieping, W.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures are based on a total of 3537 distance restraints (where 3145 were unambiguous and 392 ambiguous),111 phi torsion angles and 34 hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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