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- PDB-1tzv: T. maritima NusB, P3121, Form 1 -

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Basic information

Entry
Database: PDB / ID: 1tzv
TitleT. maritima NusB, P3121, Form 1
ComponentsN utilization substance protein B homolog
KeywordsTRANSCRIPTION / N-utilization substance / NusB / RNA-protein interaction / transcriptional antitermination / transcription regulation
Function / homology
Function and homology information


transcription antitermination / DNA-templated transcription termination / RNA binding / cytosol
Similarity search - Function
N-utilizing Substance Protein B Homolog; Chain A / NusB-like / NusB antitermination factor / NusB/RsmB/TIM44 / NusB family / NusB-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcription antitermination protein NusB
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBonin, I. / Robelek, R. / Benecke, H. / Urlaub, H. / Bacher, A. / Richter, G. / Wahl, M.C.
CitationJournal: Biochem.J. / Year: 2004
Title: Crystal structures of the antitermination factor NusB from Thermotoga maritima and implications for RNA binding
Authors: Bonin, I. / Robelek, R. / Benecke, H. / Urlaub, H. / Bacher, A. / Richter, G. / Wahl, M.C.
History
DepositionJul 12, 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 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N utilization substance protein B homolog


Theoretical massNumber of molelcules
Total (without water)17,0041
Polymers17,0041
Non-polymers00
Water5,188288
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.200, 60.200, 87.724
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-351-

HOH

21A-371-

HOH

31A-417-

HOH

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Components

#1: Protein N utilization substance protein B homolog / NusB Protein


Mass: 17003.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: nusb, TM1765 / Plasmid: pNCO113, pNOC113-tmanusb / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9X286
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.5 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: ammonium acetate, sodium phosphate, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 1, 2002
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 41043 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 18.5 Å2 / Rsym value: 0.072 / Net I/σ(I): 38.1
Reflection shellResolution: 1.35→1.45 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.358 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1EYV

1eyv


Resolution: 1.35→19.71 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1049093.51 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2049 5 %RANDOM
Rwork0.199 ---
obs0.199 40933 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.1766 Å2 / ksol: 0.345775 e/Å3
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å2-0.97 Å20 Å2
2---0.68 Å20 Å2
3---1.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.35→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 0 288 1611
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it2.392
X-RAY DIFFRACTIONc_mcangle_it3.283
X-RAY DIFFRACTIONc_scbond_it4.563
X-RAY DIFFRACTIONc_scangle_it5.994
LS refinement shellResolution: 1.35→1.43 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 325 4.8 %
Rwork0.281 6452 -
obs--99.9 %
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

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