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- PDB-2lev: Structure of the DNA complex of the C-Terminal domain of Ler -

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Basic information

Entry
Database: PDB / ID: 2lev
TitleStructure of the DNA complex of the C-Terminal domain of Ler
Components
  • DNA (5'-D(*CP*CP*TP*AP*TP*CP*AP*AP*TP*TP*AP*TP*CP*GP*C)-3')
  • DNA (5'-D(*GP*CP*GP*AP*TP*AP*AP*TP*TP*GP*AP*TP*AP*GP*G)-3')
  • Ler
KeywordsTRANSCRIPTION REGULATOR/DNA / TRANSCRIPTION REGULATOR-DNA complex / Arginine-minor-groove Recognition / Horizontal gene Transfer / Indirect Readout / Nucleoid associated Protein
Function / homology
Function and homology information


nucleoid / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Histone-like protein H-NS, C-terminal domain / H-NS DNA Binding Protein / Histone-like protein H-NS, C-terminal domain superfamily / Histone-like protein H-NS / Histone-like protein H-NS, C-terminal domain / H-NS histone C-terminal domain / Domain in histone-like proteins of HNS family / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / DNA (> 10) / Ler / Transcription regulator Ler
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / SOLUTION SCATTERING / torsion angle dynamics, simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsCordeiro, T.N. / Schimdt, H. / Madrid, C. / Juarez, A. / Bernado, P. / Grisienger, C. / Garcia, J. / Pons, M.
CitationJournal: Plos Pathog. / Year: 2011
Title: Indirect DNA Readout by an H-NS Related Protein: Structure of the DNA Complex of the C-Terminal Domain of Ler.
Authors: Cordeiro, T.N. / Schmidt, H. / Madrid, C. / Juarez, A. / Bernado, P. / Griesinger, C. / Garcia, J. / Pons, M.
History
DepositionJun 23, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ler
B: DNA (5'-D(*GP*CP*GP*AP*TP*AP*AP*TP*TP*GP*AP*TP*AP*GP*G)-3')
C: DNA (5'-D(*CP*CP*TP*AP*TP*CP*AP*AP*TP*TP*AP*TP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)15,8803
Polymers15,8803
Non-polymers00
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 / 400target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Ler


Mass: 6703.369 Da / Num. of mol.: 1 / Fragment: sequence database residues 56-102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ler / Production host: Escherichia coli (E. coli) / References: UniProt: E9N650, UniProt: Q7DB51*PLUS
#2: DNA chain DNA (5'-D(*GP*CP*GP*AP*TP*AP*AP*TP*TP*GP*AP*TP*AP*GP*G)-3')


Mass: 4673.059 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*CP*CP*TP*AP*TP*CP*AP*AP*TP*TP*AP*TP*CP*GP*C)-3')


Mass: 4503.948 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
SOLUTION SCATTERING
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC aliphatic
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D H(CCO)NH
1623D (H)CCH-TOCSY
1713D HNHA
1813D 1H-15N TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY aliphatic
11123D 1H-13C NOESY aliphatic
11222D 1H-1H (13C-ed) NOESY
11312D 1H-1H NOESY
11422D 1H-1H (13C-fil) NOESY
11512D 1H-1H (15N/13C-fil) NOESY
11613D 15N/13C-fil/13c-ed- NOESY
11722D 1H-1H (13C-fil) TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 20 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 150 mM sodium chloride, 0.01 %(w/v) sodium azide, 0.2 mM EDTA, 100% D2O100% D2O
31 mM [U-10% 13C; U-100% 15N] CT-Ler, 2 mM LeeH A, 2 mM LeeH B, 20 mM sodium phosphate, 150 mM sodium chloride, 0.01 % (w/v) sodium azide, 0.2 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCT-Ler-1[U-100% 13C; U-100% 15N]1
2 mMLeeH_A-21
2 mMLeeH_B-31
20 mMsodium phosphate-41
20 mMsodium chloride-51
0.01 %sodium azide-61
0.2 mMEDTA-71
1 mMCT-Ler-8[U-100% 13C; U-100% 15N]2
2 mMLeeH_A-92
2 mMLeeH_B-102
20 mMsodium phosphate-112
150 mMsodium chloride-122
0.01 %sodium azide-132
0.2 mMEDTA-142
1 mMCT-Ler-15[U-10% 13C; U-100% 15N]3
2 mMLeeH_A-163
2 mMLeeH_B-173
20 mMsodium phosphate-183
150 mMsodium chloride-193
0.01 %sodium azide-203
0.2 mMEDTA-213
Sample conditionsIonic strength: 150 / pH: 5.7 / Pressure: ambient / Temperature: 298 K

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Data collection

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002
Bruker AvanceBrukerAVANCE8003
Bruker AvanceBrukerAVANCE9004
Soln scatterType: x-ray
Buffer name: 20mM sodium phosphate, 150mM NaCl, 0.2mM EDTA, 0.01%NaN3
Conc. range: 3.6 - 7.3 / Data reduction software list: PRIMUS, GNOM, CRYSOL / Detector type: 2D PHOTON COUNTING PILATUS 1M PIXEL / Mean guiner radius: 1.82 nm / Mean guiner radius esd: 0.01 nm / Num. of time frames: 4 / Protein length: 5.3 / Sample pH: 5.7 / Source beamline: X33 / Source class: N / Source type: DESY-EMBL HAMBURG OUTSTATION / Temperature: 298 K

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Zhengrong and Baxprocessing
TopSpinBruker Biospinnmr spectra acquisition
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readenergy water refinement
CARAKeller and Wuthrichchemical shift assignment
TALOSCornilescu, Delaglio and Baxprediction of protein phi and psi angles using a chemical shift database
CRYSOLSvergun D.I., Barberato C. and Koch M.H.J.fitting to experimental scattering curves
HADDOCKAlexandre Bonvindata-driven docking using cns as structure calculation engine
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmmolecular dynamics refinement
ProcheckLaskowski and MacArthurquality assessment
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
HADDOCKAlexandre Bonvinrefinement
CRYSOLSvergun D.I., Barberato C. and Koch M.H.J.refinement
ProcheckLaskowski and MacArthurrefinement
RefinementMethod: torsion angle dynamics, simulated annealing, molecular dynamics
Software ordinal: 1
Details: Protein structure calculation was performed with CYANA 2.1, The 20 lowest-energy CT-Ler conformers were further energy-refined in explicit solvent using using CNS, DNA (LeeH) was defined as ...Details: Protein structure calculation was performed with CYANA 2.1, The 20 lowest-energy CT-Ler conformers were further energy-refined in explicit solvent using using CNS, DNA (LeeH) was defined as B-DNA followed by MD water refinement, including NMR restraints. The 20 lowest-energy protein structures were selected and docked onto LeeH using intermolecular NOEs and AIRs, Final scoring against experimental NMR and SAXS data. Packing, Ramachandran apprearance. Refinement against Small-Angle X-ray Scattering (SAXS) data, Quality assessment.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 20

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