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- PDB-2kl4: NMR structure of the protein NB7804A -

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Basic information

Entry
Database: PDB / ID: 2kl4
TitleNMR structure of the protein NB7804A
ComponentsBH2032 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NB7804A / BACILLUS HALODURANS / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homologyAspartate Aminotransferase, domain 1 - #200 / Domain of unknown function DUF1801 / Domain of unknown function (DU1801) / Aspartate Aminotransferase, domain 1 / Alpha-Beta Complex / Alpha Beta / BH2032 protein
Function and homology information
Biological speciesBacillus halodurans (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 6
AuthorsMohanty, B. / Geralt, M. / Augustyniak, W. / Serrano, P. / Horst, R. / Wilson, I.A. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Solution structure of the protein NB7804A from Bacillus Halodurans
Authors: Mohanty, B. / Geralt, M. / Augustyniak, W. / Serrano, P. / Horst, R. / Wilson, I.A. / Wuthrich, K.
History
DepositionJun 30, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: 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_oper_list
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
Revision 1.3Feb 1, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4May 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: BH2032 protein


Theoretical massNumber of molelcules
Total (without water)13,5231
Polymers13,5231
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80CYANA TARGET FUNCTION
RepresentativeModel #1closest to the average

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Components

#1: Protein BH2032 protein


Mass: 13523.146 Da / Num. of mol.: 1 / Fragment: sequence database residues 1-115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: BH2032 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KB96

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D [15N,1H]-HSQC
1212D [13C,1H]-HSQC
1314D-APSY-HACANH
1415D-APSY-(HA)CA(CO)NH
1515D-APSY-CBCA(CO)NH
1613D 15N-RESOLVED [1H,1H]-NOESY
1713D 13C-RESOLVED [1H,1H]-NOESY (ALIPHATIC 13C)
1813D 13C-RESOLVED [1H,1H]-NOESY (AROMATIC 13C)

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Sample preparation

DetailsContents: 0.0045 M [U-2H] D10-DTT, 0.025 M sodium phosphate, 0.050 M sodium chloride, 0.03 % sodium azide, 0.0005 M DTT, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
4.5 mMD10-DTT-1[U-2H]1
25 mMsodium phosphate-21
50 mMsodium chloride-31
0.03 %sodium azide-41
0.5 mMDTT-51
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002

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Processing

NMR software
NameVersionDeveloperClassification
UNIO1.0.2Herrmann and Wuthrichpeak picking
UNIO1.0.2Herrmann and Wuthrichnoe assignment
UNIO1.0.2Herrmann and Wuthrichstructure calculation
UNIO1.0.2Herrmann and Wuthrichchemical shift assignment
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
CARAKeller and Wuthrichpeak picking
TopSpin1.3Bruker Biospincollection
TopSpin2.1Bruker Biospincollection
TopSpin1.3Bruker Biospindata analysis
TopSpin2.1Bruker Biospindata analysis
OPALLuginbuhl, Guntert, Billeter and Wuthrichrefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: OPALp for energy minimization
NMR constraintsNOE constraints total: 2117 / NOE intraresidue total count: 539 / NOE long range total count: 665 / NOE medium range total count: 216 / NOE sequential total count: 559
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: CYANA TARGET FUNCTION / Conformers calculated total number: 80 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 3 Å

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