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- PDB-2jne: NMR structure of E.coli YfgJ modelled with two Zn+2 bound. Northe... -

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Basic information

Entry
Database: PDB / ID: 2jne
TitleNMR structure of E.coli YfgJ modelled with two Zn+2 bound. Northeast Structural Genomics Consortium Target ER317.
ComponentsHypothetical protein yfgJHypothesis
KeywordsMETAL BINDING PROTEIN / C4 / C3H / C7H / zinc fingers / two zinc / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyRubredoxin-like / YfgJ-like / DUF1407/YfgJ-like / DUF1407/YfgJ-like superfamily / zinc-ribbons / bacterial-type flagellum-dependent swarming motility / Ribbon / Mainly Beta / Uncharacterized protein YfgJ
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsRamelot, T.A. / Cort, J.R. / Yee, A.A. / Semesi, A. / Lukin, J.A. / Arrowsmith, C.H. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: NMR structure of E.coli YfgJ bound to two Zn+2.
Authors: Ramelot, T.A. / Cort, J.R. / Yee, A.A. / Arrowsmith, C.H. / Kennedy, M.A.
History
DepositionJan 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _audit_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software / 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.deposit_site / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein yfgJ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6233
Polymers11,4921
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100closest to the average
RepresentativeModel #1closest to the average

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Components

#1: Protein Hypothetical protein yfgJ / Hypothesis


Mass: 11492.293 Da / Num. of mol.: 1 / Fragment: sequence database residues 13-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yfgJ / Production host: Escherichia coli (E. coli) / References: UniProt: P76575
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 1H-15N NOESY

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Sample preparation

DetailsContents: 1 mM [U-100% 13C] protein, 10 mM TRIS, 250 mM sodium chloride, 10 uM ZINC ION, 10 mM DTT, 0.01 % sodium azide, 95% H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMprotein[U-100% 13C]1
10 mMTRIS1
250 mMsodium chloride1
10 uMZINC ION1
10 mMDTT1
0.01 %sodium azide1
Sample conditionsIonic strength: 250 / pH: 7.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
AutoStructure2.1.1Huang, Swapana, Rajan, Ke, Xia, Shukla, Inouye and Montelionedata analysis
X-PLOR NIH2.15.0Schwieters, Kuszewski, Tjandra and Clorestructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky3.1Goddardpeak picking
NMRPipelinux9Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: simulated annealling using nih xplor, followed by cns water refinement.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: closest to the average / Conformers calculated total number: 100 / Conformers submitted total number: 20

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