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- PDB-2kgo: Solution NMR structure of Zn finger protein YBIL from Escherichia... -

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Basic information

Entry
Database: PDB / ID: 2kgo
TitleSolution NMR structure of Zn finger protein YBIL from Escherichia coli. NESG target ET107, OCSP target EC0402
ComponentsUncharacterized protein ybiI
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Zn finger / partially disordered / structural proteomics / Metal-binding / Zinc-finger / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Ontario Centre for Structural Proteomics / OCSP
Function / homologyZinc finger, DksA/TraR C4-type conserved site / Zinc finger, DksA/TraR C4-type, bacteria / Prokaryotic dksA C4-type zinc finger. / positive regulation of secondary metabolite biosynthetic process / Zinc finger, DksA/TraR C4-type / Prokaryotic dksA/traR C4-type zinc finger / Prokaryotic dksA C4-type zinc finger profiles. / zinc ion binding / Uncharacterized protein YbiI
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model 1
AuthorsGutmanas, A. / Yee, A. / Lemak, A. / Fares, C. / Guido, V. / Arrowsmith, C.H. / Northeast Structural Genomics Consortium (NESG) / Ontario Centre for Structural Proteomics (OCSP)
CitationJournal: To be Published
Title: Zn-finger protein YBIL from E. coli
Authors: Gutmanas, A. / Yee, A. / Lemak, A. / Fares, C. / Arrowsmith, C.H.
History
DepositionMar 13, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 8, 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 ybiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0062
Polymers11,9401
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein ybiI


Mass: 11940.175 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b0803, JW0788, ybiI, ybil / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P41039
#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 CT-HSQC
1413D CBCA(CO)NH
1513D HNCO
1613D HNCA
1713D C(CO)NH TOCSY
1813D HBHA(CO)NH
1913D H(CCO)NH TOCSY
11013D H(C)CH-TOCSY aliphatic
11113D (H)CCH-TOCSY aliphatic
11213D 15N-NOESY-HSQC
11313D 13C-NOESY-HSQC aliphatic
11413D 13C-NOESY-HSQC aromatic
11513D H(C)CH-TOCSY aromatic
11612D 1H-15N HSQC long range
11712D (HB)CB(CGCD)HD
11812D (HB)CB(CGCDCE)HE
NMR detailsText: 1. THE 3 NOESY AND 3 HCCH-TYPE TOCSY SPECTRA WERE COLLECTED WITH NON-UNIFORM (NON-LINEAR) SAMPLING AND PROCESSED WITH MDDNMR SOFTWARE. 2. RESIDUES 54-90 FORM A GLOBULAR ZN2+ BINDING MODULE. 3. ...Text: 1. THE 3 NOESY AND 3 HCCH-TYPE TOCSY SPECTRA WERE COLLECTED WITH NON-UNIFORM (NON-LINEAR) SAMPLING AND PROCESSED WITH MDDNMR SOFTWARE. 2. RESIDUES 54-90 FORM A GLOBULAR ZN2+ BINDING MODULE. 3. RESIDUES 1-27, 48-53 AND 91-108 ARE DISORDERED, AS JUDGED BY LACK OF LONG- AND MEDIUM- RANGE NOES AND RANDOM COIL INDEX AND CHEMICAL SHIFT INDEX PREDICTIONS. 4. HELIX 2 (RESIDUES 37-47), WHILE NOT PART OF THE GLOBULAR DOMAIN, IS SUPPORTED BY BOTH NOE AND CHEMICAL SHIFT DATA (RANDOM COIL INDEX, CHEMICAL SHIFT INDEX, TALOS). 5. RESIDUES 28-36 (HELIX 1) APPEAR TO FORM A NASCENT HELIX WITH SOME MEDIUM RANGE NOES, BUT CHEMICAL SHIFT DATA (RANDOM COIL INDEX, CHEMICAL SHIFT INDEX) SUGGEST IT MAY NOT BE A STABLE HELIX.

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Sample preparation

DetailsContents: 0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM ...Contents: 0.7-1 mM [U-100% 13C; U-100% 15N] protein YBIL-1, 10 uM Zn sulfate-2, 10 mM [U-2H] DTT-3, 10 mM [U-2H] TRIS-4, 300 mM sodium chloride-5, 0.01 % sodium azide-6, 1 mM benzamidine-7, 1 mM Roche inhibitor-8, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMprotein YBIL-1[U-100% 13C; U-100% 15N]0.7-11
10 uMZn sulfate-21
10 mMDTT-3[U-2H]1
10 mMTRIS-4[U-2H]1
300 mMsodium chloride-51
0.01 %sodium azide-61
1 mMbenzamidine-71
1 mMRoche inhibitor-81
Sample conditionsIonic strength: 0.300 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
ABACUSA. Lemakchemical shift assignment
ABACUSA. Lemakdata analysis
TALOSCornilescu, Delaglio and Baxgeometry optimization
Analysis2.06CCPNdata analysis
Analysis2.06CCPNpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MddNMRV. Orekhov, I. Ibraghimovprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: water bath
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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