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- PDB-1tzx: T. maritima NusB, P3221 -

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Basic information

Entry
Database: PDB / ID: 1tzx
TitleT. maritima NusB, P3221
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
CITRIC ACID / Transcription antitermination protein NusB
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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: Advisory / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: N utilization substance protein B homolog
B: N utilization substance protein B homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3914
Polymers34,0072
Non-polymers3842
Water4,324240
1
A: N utilization substance protein B homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1962
Polymers17,0041
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N utilization substance protein B homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1962
Polymers17,0041
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.011, 60.011, 172.442
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-678-

HOH

21B-590-

HOH

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Components

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


Mass: 17003.572 Da / Num. of mol.: 2
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: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 50.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: Sodium citrate, pH 7.9, 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: 1.72→57.74 Å / Num. obs: 39263 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 33.3 Å2 / Rsym value: 0.069 / Net I/σ(I): 37.6
Reflection shellResolution: 1.72→1.82 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.373 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1EYV

1eyv


Resolution: 1.72→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.192 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.119 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24937 1972 5 %RANDOM
Rwork0.21702 ---
obs0.21862 37203 99.62 %-
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: 25.194 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.11 Å20 Å2
2---0.23 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.72→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 26 240 2642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212415
X-RAY DIFFRACTIONr_bond_other_d0.0020.022300
X-RAY DIFFRACTIONr_angle_refined_deg1.0821.9863237
X-RAY DIFFRACTIONr_angle_other_deg0.82335321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3755280
X-RAY DIFFRACTIONr_chiral_restr0.070.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022608
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02512
X-RAY DIFFRACTIONr_nbd_refined0.2180.2556
X-RAY DIFFRACTIONr_nbd_other0.2330.22661
X-RAY DIFFRACTIONr_nbtor_other0.0790.21418
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2150
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.070.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3580.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.214
X-RAY DIFFRACTIONr_mcbond_it1.30131407
X-RAY DIFFRACTIONr_mcangle_it2.15942272
X-RAY DIFFRACTIONr_scbond_it1.52531008
X-RAY DIFFRACTIONr_scangle_it2.54965
LS refinement shellResolution: 1.718→1.763 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.329 145
Rwork0.263 2697
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.444-0.29580.75692.10420.22472.1810.03150.16740.07-0.01940.01110.05910.21310.0931-0.04260.0544-0.0003-0.00530.05810.00670.001836.149227.09131.0244
21.8932-0.16140.76061.87020.18772.27280.08240.00890.1570.14180.0386-0.05470.12320.1187-0.1210.04220.01890.00060.0303-0.00810.040245.798833.878627.2125
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1422 - 142
2X-RAY DIFFRACTION2BB2 - 1422 - 142

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