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- PDB-1tzt: T. maritima NusB, P21 -

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Basic information

Entry
Database: PDB / ID: 1tzt
TitleT. maritima NusB, P21
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: 1.55 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)34,1994
Polymers34,0072
Non-polymers1922
Water7,062392
1
A: N utilization substance protein B homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1002
Polymers17,0041
Non-polymers961
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)17,1002
Polymers17,0041
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.714, 34.354, 74.322
Angle α, β, γ (deg.)90.00, 94.18, 90.00
Int Tables number4
Space group name H-MP1211

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: ammonium sulfate, PEG 8000, pH 6.3, 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: 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: 1.55→30 Å / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 26.2 Å2 / Rsym value: 0.072 / Net I/σ(I): 28.7
Reflection shellResolution: 1.55→1.65 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.616 / % possible all: 95.2

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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: 1.55→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.021 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE WAS REFINED ALSO WITH CNS 1.0.
RfactorNum. reflection% reflectionSelection details
Rfree0.25096 2165 5.1 %RANDOM
Rwork0.23492 ---
all0.23574 41944 --
obs0.23574 40560 96.69 %-
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: 21.632 Å2
Baniso -1Baniso -2Baniso -3
1--3.38 Å20 Å20.13 Å2
2--0.22 Å20 Å2
3---3.18 Å2
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 10 392 2764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212351
X-RAY DIFFRACTIONr_bond_other_d0.0020.022235
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.9783153
X-RAY DIFFRACTIONr_angle_other_deg0.835159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4745280
X-RAY DIFFRACTIONr_chiral_restr0.0680.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022556
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02498
X-RAY DIFFRACTIONr_nbd_refined0.2190.2637
X-RAY DIFFRACTIONr_nbd_other0.2380.22652
X-RAY DIFFRACTIONr_nbtor_other0.0850.21398
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2170
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3150.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.213
X-RAY DIFFRACTIONr_mcbond_it1.41731404
X-RAY DIFFRACTIONr_mcangle_it2.18242259
X-RAY DIFFRACTIONr_scbond_it1.5763947
X-RAY DIFFRACTIONr_scangle_it2.3424894
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.35 164
Rwork0.351 2914
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)
12.7032-0.1279-0.0210.7206-0.00780.30450.02510.32030.027-0.0143-0.06650.02220.00270.11620.04140.1110.01330.00040.10350.03320.010812.36-0.37331.028
24.06560.09410.62810.67610.05520.2104-0.00750.37430.03890.0006-0.02480.02180.0081-0.01820.03230.10570.0060.00250.09620.00080.010414.7888-7.1347-6.0462
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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