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- PDB-3d3c: Structural and functional analysis of the E. coli NusB-S10 transc... -

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Basic information

Entry
Database: PDB / ID: 3d3c
TitleStructural and functional analysis of the E. coli NusB-S10 transcription antitermination complex.
Components
  • 30S ribosomal protein S10
  • N utilization substance protein B
KeywordsTRANSCRIPTION / NusB / S10 / NusE / Nut / phage lambda / lambda N antitermination / rrn antitermination / transcription regulation / RNA-binding / Transcription termination / Ribonucleoprotein / Ribosomal protein
Function / homology
Function and homology information


transcription antitermination factor activity, RNA binding / regulation of DNA-templated transcription elongation / transcription elongation factor complex / transcription antitermination / DNA-templated transcription termination / ribosome biogenesis / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding ...transcription antitermination factor activity, RNA binding / regulation of DNA-templated transcription elongation / transcription elongation factor complex / transcription antitermination / DNA-templated transcription termination / ribosome biogenesis / small ribosomal subunit / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / structural constituent of ribosome / RNA binding / cytoplasm / 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 / Ribosomal protein S10 / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S10 ...N-utilizing Substance Protein B Homolog; Chain A / NusB-like / NusB antitermination factor / NusB/RsmB/TIM44 / NusB family / NusB-like superfamily / Ribosomal protein S10 / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S10 / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transcription antitermination protein NusB / Small ribosomal subunit protein uS10
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLuo, X. / Wahl, M.C.
CitationJournal: Mol.Cell / Year: 2008
Title: Structural and functional analysis of the E. coli NusB-S10 transcription antitermination complex.
Authors: Luo, X. / Hsiao, H.H. / Bubunenko, M. / Weber, G. / Court, D.L. / Gottesman, M.E. / Urlaub, H. / Wahl, M.C.
History
DepositionMay 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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
J: 30S ribosomal protein S10
B: N utilization substance protein B
K: 30S ribosomal protein S10
C: N utilization substance protein B
L: 30S ribosomal protein S10


Theoretical massNumber of molelcules
Total (without water)76,4716
Polymers76,4716
Non-polymers00
Water3,549197
1
A: N utilization substance protein B
J: 30S ribosomal protein S10


Theoretical massNumber of molelcules
Total (without water)25,4902
Polymers25,4902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N utilization substance protein B
K: 30S ribosomal protein S10


Theoretical massNumber of molelcules
Total (without water)25,4902
Polymers25,4902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N utilization substance protein B
L: 30S ribosomal protein S10


Theoretical massNumber of molelcules
Total (without water)25,4902
Polymers25,4902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.000, 113.000, 267.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-165-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12J
22K
32L

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULYSLYSAA2 - 1394 - 141
21GLUGLULYSLYSBC2 - 1394 - 141
31GLUGLULYSLYSCE2 - 1394 - 141
12METMETGLYGLYJB1 - 826 - 87
22METMETGLYGLYKD1 - 826 - 87
32METMETGLYGLYLF1 - 826 - 87

NCS ensembles :
ID
1
2

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Components

#1: Protein N utilization substance protein B / Protein nusB


Mass: 15838.095 Da / Num. of mol.: 3 / Mutation: K2E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: nusB, ssyB, b0416, JW0406 / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) / References: UniProt: P0A780
#2: Protein 30S ribosomal protein S10


Mass: 9652.153 Da / Num. of mol.: 3 / Mutation: A86D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpsJ, nusE, b3321, JW3283 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0A7R5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 46-67 OF CHAINS J,K,L ARE REPLACED WITH A SINGLE SER.

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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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.1 M Tris-HCl, pH 7.1, 0.2 M ammonium sulfate, 25 % PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9763 Å
DetectorType: PILATUS 6M / Detector: PIXEL / Date: Sep 7, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 39315 / Num. obs: 26358 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Rmerge(I) obs: 0.141 / Rsym value: 0.141 / Net I/σ(I): 16.2
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 8.3 / Rsym value: 0.314 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3D3B

3d3b


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.886 / SU B: 22.962 / SU ML: 0.252 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / ESU R: 0.78 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27988 1317 5 %RANDOM
Rwork0.21766 ---
obs0.22078 25020 100 %-
all-38823 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.323 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5308 0 0 197 5505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225382
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.091.9867279
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77423.571252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.17715984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4781557
X-RAY DIFFRACTIONr_chiral_restr0.0740.2845
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024026
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.22525
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.23709
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3430.2117
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2841.53440
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.51325411
X-RAY DIFFRACTIONr_scbond_it0.44932124
X-RAY DIFFRACTIONr_scangle_it0.84.51868
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1079medium positional0.850.5
12B1079medium positional0.720.5
13C1079medium positional0.850.5
21J647medium positional0.890.5
22K647medium positional1.010.5
23L647medium positional0.940.5
11A1079medium thermal1.372
12B1079medium thermal2.432
13C1079medium thermal2.632
21J647medium thermal0.952
22K647medium thermal2.472
23L647medium thermal2.612
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 96 -
Rwork0.295 1825 -
obs--100 %
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)
17.5412-1.94420.19424.8988-0.09843.34340.01710.389-0.2403-0.2379-0.0067-0.67760.30890.4417-0.0104-0.11080.02470.0912-0.2223-0.07330.076910.43326.14216.957
24.4367-2.38581.44284.8674-0.35952.2310.1795-0.0095-0.2942-0.1670.0478-0.02760.211-0.1372-0.2272-0.1232-0.0476-0.0282-0.2456-0.0217-0.2005-27.3814.55421.706
36.8139-2.9770.09075.2983-0.07122.0421-0.2784-0.32040.42470.34070.21510.6373-0.071-0.64510.0633-0.10.10760.0710.1649-0.02240.025-61.4738.97416.982
46.7595-1.3905-2.40195.11381.28123.0725-0.05320.12490.3714-0.1090.0514-0.2022-0.1650.08670.0018-0.0977-0.0346-0.0295-0.2889-0.01020.1114.30146.14528.346
54.23320.3874-0.50945.47450.19984.49580.06840.19490.149-0.2043-0.05230.1679-0.1796-0.2771-0.0162-0.08660.0096-0.0169-0.18350.0091-0.2113-22.77637.315.481
65.6457-4.8702-0.93336.62362.02795.94730.14350.2615-0.1907-0.4091-0.32580.3452-0.2672-0.40890.1823-0.11290.0305-0.02680.0174-0.0211-0.0274-53.6727.885-3.07
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1394 - 141
2X-RAY DIFFRACTION2BC2 - 1394 - 141
3X-RAY DIFFRACTION3CE2 - 1394 - 141
4X-RAY DIFFRACTION4JB-2 - 823 - 87
5X-RAY DIFFRACTION5KD-4 - 821 - 87
6X-RAY DIFFRACTION6LF-4 - 821 - 87

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