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- PDB-1lv3: Solution NMR Structure of Zinc Finger Protein yacG from Escherich... -

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Basic information

Entry
Database: PDB / ID: 1lv3
TitleSolution NMR Structure of Zinc Finger Protein yacG from Escherichia coli. Northeast Structural Genomics Consortium Target ET92.
ComponentsHYPOTHETICAL PROTEIN YacG
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / zinc finger / rubredoxin knuckle / C4 tetrahedral Zn+2 / antiparallel beta strand and alpha helix / NESG Project / ET92 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity / regulation of DNA-templated transcription / zinc ion binding
Similarity search - Function
DNA gyrase inhibitor YacG / DNA gyrase inhibitor YacG / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Zinc finger, NHR/GATA-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA gyrase inhibitor YacG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsRamelot, T.A. / Cort, J.R. / Yee, A.A. / Semesi, A. / Edwards, A.M. / Arrowsmith, C.H. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2002
Title: NMR structure of the Escherichia coli protein YacG: a novel sequence motif in the zinc-finger family of proteins.
Authors: Ramelot, T.A. / Cort, J.R. / Yee, A.A. / Semesi, A. / Edwards, A.M. / Arrowsmith, C.H. / Kennedy, M.A.
History
DepositionMay 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 5, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_representative / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_planes / pdbx_validate_torsion / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_nmr_representative.conformer_id / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.value / _pdbx_validate_planes.rmsd / _pdbx_validate_torsion.PDB_model_num / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_ref_seq_dif.details
Revision 2.1Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2May 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: HYPOTHETICAL PROTEIN YacG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6612
Polymers7,5951
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with favorable non-bond energy
RepresentativeModel #1closest to the average

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Components

#1: Protein HYPOTHETICAL PROTEIN YacG


Mass: 7595.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yacG / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A8H8
#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
1114D 13C-separated NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
141HNHA
1512H exchange

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Sample preparation

DetailsContents: 2mM YacG U-15N, 450 mM NaCl, 25 mM Na2HPO4, 10 mM DTT
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 450 mM salt, 25 mM phosphate buffer / pH: 6.5 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
X-PLOR3.84structure solution
Felix98processing
VNMRcollection
Sparkydata analysis
X-PLOR3.84Brunger, A.T.refinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 396 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE CONSTRAINTS: TOTAL = 367; ZN RESTRAINTS 10; INTRA-RESIDUE [I=J] = 93; SEQUENTIAL [(I-J)=1] ...Details: THE STRUCTURES ARE BASED ON A TOTAL OF 396 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS: DISTANCE CONSTRAINTS: TOTAL = 367; ZN RESTRAINTS 10; INTRA-RESIDUE [I=J] = 93; SEQUENTIAL [(I-J)=1] = 120; MEDIUM RANGE [1<(I-J)<5] = 52; LONG RANGE [(I-J)>=5] = 86; NUMBER OF DISTANCE CONSTRAINTS PER RESIDUE (RESIDUES 4-40)= 9.8; DIHEDRAL-ANGLE CONSTRAINTS = 29 (16 PHI, 13 PSI); TOTAL HYDROGEN BOND CONSTRAINTS = 6 (2 PER H-BOND); TOTAL NUMBER OF CONSTRAINTS PER RESIDUE (4-40)= 10.6; NUMBER OF LONG RANGE CONSTRAINTS PER RESIDUE = 2.6; NUMBER OF STRUCTURES COMPUTED = 40; NUMBER OF STRUCTURES USED = 20. AVERAGE RESIDUAL CONSTRAINT VIOLATIONS: DISTANCE VIOLATIONS >0.0 ANG = 20. AVERAGE R.M.S. DISTANCE VIOLATION = 0.011 ANG. MAXIMUM NUMBER OF DISTANCE VIOLATIONS 26. AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0 DEG = 0.8; MAX NUMBER OF ANGLE VIOLATION = 2 DEG; AVERAGE R.M.S. ANGLE VIOLATION = 0.11 DEG. RMSD VALUES: BACKBONE ATOMS (N,C,C') OF RESIDUES (4-40) = 0.46 ANG; BACKBONE ATOMS(N,C,C') OF SECONDARY STRUCTURE RESIDUES (6-17, 30-37) = 0.22 ANG; ALL HEAVY ATOMS OF RESIDUES (4-40) = 1.01 ANG; ALL HEAVY ATOMS OF SECONDARY STRUCTURE RESIDUES = 0.77 ANG. PROCHECK USING RESIDUES (4-40): MOST FAVORED REGIONS = 76%; ADDITIONAL ALLOWED REGIONS = 16%; GENEROUSLY ALLOWED REGIONS = 4%; DISALLOWED REGIONS = 4%. PROCHECK USING SECONDARY STRUCTURE RESIDUES (6-17, 30-37): MOST FAVOREDREGIONS = 95%; ADDITIONAL ALLOWED REGIONS = 5%; GENEROUSLY ALLOWED REGIONS =0%; DISALLOWED REGIONS = 0%.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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