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- PDB-2nb9: Solution structure of ZitP zinc finger -

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Basic information

Entry
Database: PDB / ID: 2nb9
TitleSolution structure of ZitP zinc finger
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / zinc finger
Function / homologyZinc finger/thioredoxin putative / zinc-ribbon domain / membrane => GO:0016020 / Znf/thioredoxin_put domain-containing protein
Function and homology information
Biological speciesCaulobacter crescentus (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsCampagne, S. / Berge, M. / Viollier, P.H. / Allain, F.H.-T.
CitationJournal: Elife / Year: 2016
Title: Modularity and determinants of a (bi-)polarization control system from free-living and obligate intracellular bacteria.
Authors: Berge, M. / Campagne, S. / Mignolet, J. / Holden, S. / Theraulaz, L. / Manley, S. / Allain, F.H. / Viollier, P.H.
History
DepositionFeb 1, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _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 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5652
Polymers5,4991
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 / 30structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Uncharacterized protein


Mass: 5499.287 Da / Num. of mol.: 1 / Fragment: residues 33-75
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Strain: ATCC 19089 / CB15 / Gene: CC_2215 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9A679
#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
Details: Solution structure of the zinc finger domain of ZitP from Caulobacter crescentus
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HNCO
1713D H(CCO)NH
1813D C(CO)NH
1913D 1H-15N NOESY
11013D 1H-13C NOESY aliphatic
11113D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] protein, 1 mM ZINC ION, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity_1-1[U-100% 13C; U-100% 15N]1
1 mMZINC ION-21
Sample conditionsIonic strength: 50 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3Bruker Biospincollection
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmanrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 440 / NOE intraresidue total count: 135 / NOE medium range total count: 154 / NOE sequential total count: 131 / Protein phi angle constraints total count: 31 / Protein psi angle constraints total count: 31
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0.7 ° / Maximum upper distance constraint violation: 0.28 Å / Torsion angle constraint violation method: AMBER

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