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- PDB-2kts: NMR structure of the protein NP_415897.1 -

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Basic information

Entry
Database: PDB / ID: 2kts
TitleNMR structure of the protein NP_415897.1
ComponentsHeat shock protein hslJHeat shock response
KeywordsCHAPERONE / NP_415897.1 / JCSG / Stress response / Structural Genomics / Protein Structure Initiative / Joint Center for Structural Genomics / PSI
Function / homologyDomain of unknown function DUF306, Meta/HslJ / HslJ-like superfamily / META domain / Lipocalin - #270 / Lipocalin / response to heat / Beta Barrel / Mainly Beta / Heat shock protein HslJ
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average
AuthorsSerrano, P. / Jaudzems, K. / Geralt, M. / Horst, R. / Wuthrich, K. / Wilson, I.A. / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: NMR structure of the protein NP_415897.1
Authors: Serrano, P. / Jaudzems, K. / Geralt, M. / Horst, R. / Wilson, I.A. / Wuthrich, K.
History
DepositionFeb 6, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Structure summary
Revision 1.3Aug 10, 2011Group: Derived calculations
Revision 1.4Mar 20, 2013Group: Other
Revision 1.5Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.6Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock protein hslJ


Theoretical massNumber of molelcules
Total (without water)12,8471
Polymers12,8471
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)19 / 80target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Heat shock protein hslJ / Heat shock response


Mass: 12846.747 Da / Num. of mol.: 1 / Fragment: sequence database residues 25-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: k12 / Gene: hslJ, ydbI, b1379, JW1374 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): (DE3) / References: UniProt: P52644

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: NMR structure of the protein NP_415897.1
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-13C NOESY (Ali)
1513D 1H-13C NOESY (Aro)
161APSY 5D-CBCA(CO)NH
171APSY 5D-(HA)CA(CO)NH
181APSY 4D-HACANH

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Sample preparation

DetailsContents: 1.2 mM [U-98% 13C; U-98% 15N] NP_415897.1-1, 20 mM sodium phosphate-2, 50 mM sodium chloride-3, 0.05 % sodium azide-4, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMNP_415897.1-1[U-98% 13C; U-98% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
0.05 %sodium azide-41
Sample conditionsIonic strength: 0.1 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CARAKeller and Wuthrichchemical shift assignment
TopSpinBruker Biospinprocessing
TopSpinBruker Biospincollection
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
UNIOHerrmann and Wuthrichchemical shift assignment
UNIOHerrmann and Wuthrichpeak picking
UNIOHerrmann and Wuthrichstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 19

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