[English] 日本語
Yorodumi
- PDB-1tzu: T. maritima NusB, P212121 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tzu
TitleT. maritima NusB, P212121
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: 1.85 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: Advisory / Data collection ...Advisory / 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 / pdbx_validate_polymer_linkage / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_polymer_linkage.label_alt_id_1 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: N utilization substance protein B homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1002
Polymers17,0041
Non-polymers961
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.766, 59.600, 64.322
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 2-propanol, PEG 4000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
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: 1.85→30 Å / Num. obs: 11016 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 27.6 Å2 / Rsym value: 0.068 / Net I/σ(I): 20.6
Reflection shellResolution: 1.85→1.95 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.253 / % possible all: 94.8

-
Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1EYV

1eyv


Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.229 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.218 / ESU R Free: 0.172 / 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
Rfree0.25253 526 4.8 %RANDOM
Rwork0.2244 ---
obs0.22575 10471 94.87 %-
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: 24.943 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2---4.28 Å20 Å2
3---3.29 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 0 5 137 1317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211188
X-RAY DIFFRACTIONr_bond_other_d0.0020.021100
X-RAY DIFFRACTIONr_angle_refined_deg1.0151.9811591
X-RAY DIFFRACTIONr_angle_other_deg0.79132532
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6265139
X-RAY DIFFRACTIONr_chiral_restr0.0570.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021291
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02255
X-RAY DIFFRACTIONr_nbd_refined0.3070.2362
X-RAY DIFFRACTIONr_nbd_other0.2170.21316
X-RAY DIFFRACTIONr_nbtor_other0.0840.2746
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.258
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0780.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.217
X-RAY DIFFRACTIONr_mcbond_it1.2653705
X-RAY DIFFRACTIONr_mcangle_it2.42141134
X-RAY DIFFRACTIONr_scbond_it3.46483
X-RAY DIFFRACTIONr_scangle_it5.8279457
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 34
Rwork0.295 728
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)
10.7073-0.8399-0.20123.25781.30170.834-0.03760.0150.0603-0.2309-0.05410.19520.0133-0.05370.09170.1142-0.0138-0.05330.11330.00020.0252-5.437730.413519.0749
2-1.5413-2.0396-1.78355.12450.09030.6769-0.24680.1001-0.04760.02990.5698-0.40920.26830.1834-0.32310.06470.0689-0.00170.116-0.01420.132211.307821.178427.7711
30.57781.1856-0.06432.61530.48830.5119-0.03790.00520.01990.11920.144-0.17280.1180.0517-0.10610.07530.0128-0.02920.1176-0.00620.06655.063631.752131.7763
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 563 - 56
2X-RAY DIFFRACTION2AA57 - 7757 - 77
3X-RAY DIFFRACTION3AA78 - 14278 - 142

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more