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- PDB-1u9l: Structural basis for a NusA- protein N interaction -

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Basic information

Entry
Database: PDB / ID: 1u9l
TitleStructural basis for a NusA- protein N interaction
Components
  • Lambda N
  • Transcription elongation protein nusA
KeywordsRNA BINDING PROTEIN / Escherichia coli NusA / Phage lambda protein N / Regulation of RNA binding / Transcription antitermination
Function / homology
Function and homology information


bacterial-type RNA polymerase core enzyme binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribosome biogenesis / protein complex oligomerization / DNA-binding transcription factor activity / protein domain specific binding / nucleotide binding ...bacterial-type RNA polymerase core enzyme binding / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribosome biogenesis / protein complex oligomerization / DNA-binding transcription factor activity / protein domain specific binding / nucleotide binding / RNA binding / cytosol / cytoplasm
Similarity search - Function
Transcription termination factor NusA, C-terminal duplication / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like KH domain / Transcription termination/antitermination protein NusA, bacterial / RNA-binding domain, S1 / Type-1 KH domain profile. ...Transcription termination factor NusA, C-terminal duplication / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like KH domain / Transcription termination/antitermination protein NusA, bacterial / RNA-binding domain, S1 / Type-1 KH domain profile. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / K homology domain superfamily, prokaryotic type / K homology domain-like, alpha/beta / Nucleic acid-binding, OB-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Transcription termination/antitermination protein NusA / Transcription termination/antitermination protein NusA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsBonin, I. / Muehlberger, R. / Bourenkov, G.P. / Huber, R. / Bacher, A. / Richter, G. / Wahl, M.C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: Structural basis for the interaction of Escherichia coli NusA with protein N of phage lambda
Authors: Bonin, I. / Muehlberger, R. / Bourenkov, G.P. / Huber, R. / Bacher, A. / Richter, G. / Wahl, M.C.
History
DepositionAug 10, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Transcription elongation protein nusA
B: Transcription elongation protein nusA
C: Lambda N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5594
Polymers16,3623
Non-polymers1971
Water2,666148
1
A: Transcription elongation protein nusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9722
Polymers7,7751
Non-polymers1971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcription elongation protein nusA
C: Lambda N


Theoretical massNumber of molelcules
Total (without water)8,5882
Polymers8,5882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.787, 69.787, 67.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Transcription elongation protein nusA / N utilization substance protein A / L factor


Mass: 7774.664 Da / Num. of mol.: 2 / Fragment: C-terminal repeat unit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nusA / Plasmid: pNCO113 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: UniProt: P03003, UniProt: P0AFF6*PLUS
#2: Protein/peptide Lambda N


Mass: 812.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic Peptide of Lambda N residues 34-40
#3: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 0.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Ammonium sulfate, MES, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.95, 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 11, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.951
21.051
ReflectionResolution: 1.85→50 Å / Num. obs: 13388 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 30.5 Å2 / Rsym value: 0.036 / Net I/σ(I): 17.8
Reflection shellResolution: 1.85→1.95 Å / Mean I/σ(I) obs: 1.3 / Rsym value: 0.676 / % possible all: 99.4

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→19.84 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.234 / SU ML: 0.096 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.167 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 676 5 %RANDOM
Rwork0.216 ---
all0.217 ---
obs0.21659 12722 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.484 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1132 0 1 148 1281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONc_bond_d0.0040.0221103
X-RAY DIFFRACTIONc_angle_deg1.2311.9911496
X-RAY DIFFRACTIONc_mcbond_it2.8693721
X-RAY DIFFRACTIONc_mcangle_it3.88241148
X-RAY DIFFRACTIONc_scbond_it4.5224382
X-RAY DIFFRACTIONc_scangle_it6.4475348
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.366 38
Rwork0.256 924
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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