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- PDB-2jz8: Solution NMR structure of BH09830 from Bartonella henselae modele... -

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Basic information

Entry
Database: PDB / ID: 2jz8
TitleSolution NMR structure of BH09830 from Bartonella henselae modeled with one Zn+2 bound. Northeast Structural Genomics Consortium target BnR55
ComponentsUncharacterized protein BH09830
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / zinc binding / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyq5lls5 like domains / HSP40/DNAj peptide-binding domain / Zinc finger, CHCC-type / Zinc-finger domain / Sandwich / Mainly Beta / Zinc finger CHCC-type domain-containing protein / zf-CHCC domain-containing protein
Function and homology information
Biological speciesBartonella henselae str. Houston-1 (bacteria)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsDing, K. / Cort, J.R. / Wang, D. / Janjua, H. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. ...Ding, K. / Cort, J.R. / Wang, D. / Janjua, H. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of BH09830 from Bartonella henselae modeled with one Zn+2 bound.
Authors: Ding, K. / Cort, J.R. / Wang, D. / Janjua, H. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Swapna, G.V.T. / Acton, T.B. / Rost, B. / Montelione, G.T. / Kennedy, M.A.
History
DepositionDec 30, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: 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_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 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: Uncharacterized protein BH09830
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2172
Polymers10,1511
Non-polymers651
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 / 25structures with the lowest noe and bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein BH09830


Mass: 10151.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae str. Houston-1 (bacteria)
Species: Bartonella henselae / Strain: Houston 1 / Gene: BH09830 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6G326, UniProt: A0A0H3M3K8*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C Arom HSQC
1413D HNCO
1513D HN(CA)CB
1613D CBCA(CO)NH
1713D HBHA(CO)NH
1813D HNHA
1913D C(CO)NH
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY
11313D 1H-13C Arom NOESY
11424D (H)CCH NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 13C; U-100% 15N] BH09830 monomer, 50 uM DSS, 0.02 % NaN3, 100 mM DTT, 5 mM CaCl2, 100 mM NaCl, 20 mM MES, 90% H2O/10% D2O90% H2O/10% D2O
20.8 mM [U-100% 13C; U-100% 15N] BH09830 monomer, 50 uM DSS, 0.02 % NaN3, 100 mM DTT, 5 mM CaCl2, 100 mM NaCl, 20 mM MES, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMBH09830 monomer[U-100% 13C; U-100% 15N]1
50 uMDSS1
0.02 %NaN31
100 mMDTT1
5 mMCaCl21
100 mMNaCl1
20 mMMES1
0.8 mMBH09830 monomer[U-100% 13C; U-100% 15N]2
50 uMDSS2
0.02 %NaN32
100 mMDTT2
5 mMCaCl22
100 mMNaCl2
20 mMMES2
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
X-PLOR-NIH2.15.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
AutoStructure2.1.1Huang, Tejero, Powers and Montelionedata analysis
Sparky3.1Goddarddata analysis
NMRPipelinux9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
Details: DGSA using xplor NIH and then followed by cns water refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest noe and bond energy
Conformers calculated total number: 25 / Conformers submitted total number: 20

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