[English] 日本語
Yorodumi
- PDB-1npr: CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS NUSG IN C222(1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1npr
TitleCRYSTAL STRUCTURE OF AQUIFEX AEOLICUS NUSG IN C222(1)
ComponentsTranscription antitermination protein nusG
KeywordsTRANSCRIPTION / Transcription factor / NusG
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / cytosol
Similarity search - Function
N-utilization substance G protein NusG, insert domain / NusG, domain 2 / NusG, domain 2 superfamily / NusG domain II / mini-chromosome maintenance (MCM) complex, domain 2 / NusG, N-terminal domain / : / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. ...N-utilization substance G protein NusG, insert domain / NusG, domain 2 / NusG, domain 2 superfamily / NusG domain II / mini-chromosome maintenance (MCM) complex, domain 2 / NusG, N-terminal domain / : / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / SH3 type barrels. - #30 / NusG-like / Transcription termination factor nusG / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / SH3 type barrels. / KOW (Kyprides, Ouzounis, Woese) motif. / Translation protein SH3-like domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Roll / Alpha-Beta Plaits / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Transcription termination/antitermination protein NusG
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsKnowlton, J.R. / Bubunenko, M. / Andrykovitch, M. / Guo, W. / Routzhan, K.M. / Waugh, D.S. / Court, D.L. / Ji, X.
Citation
Journal: Biochemistry / Year: 2003
Title: A Spring-Loaded State of NusG in Its Functional Cycle Is Suggested by X-ray Crystallography and Supported by Site-Directed Mutants
Authors: Knowlton, J.R. / Bubunenko, M. / Andrykovitch, M. / Guo, W. / Routzhan, K.M. / Waugh, D.S. / Court, D.L. / Ji, X.
#1: Journal: Embo J. / Year: 2002
Title: Crystal structures of transcription factor NusG in light of its nucleic acid-and protein-binding activities
Authors: Steiner, T. / Kaiser, J.T. / Marinkovic, S. / Huber, R. / Wahl, M.C.
History
DepositionJan 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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
Revision 1.4Aug 30, 2023Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription antitermination protein nusG


Theoretical massNumber of molelcules
Total (without water)28,0421
Polymers28,0421
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.95, 124.58, 83.60
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Transcription antitermination protein nusG


Mass: 28041.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: NUSG OR AQ_1931 / Plasmid: pKM702 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O67757
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 4000 Hepes Glycerol Isopropanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Details: Andrykovitch, M., (2002) Acta Crystallogr., D58, 2157.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
3200 mM1dropNaCl
42 mMEDTA1drop
510 mMdithiothreitol1drop
60.085 Msodium HEPES1reservoirpH7.5
715 %glycerol1reservoir
811 %2-propanol1reservoir
920 %PEG40001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Oct 15, 2000 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.21→29.19 Å / Num. all: 17608 / Num. obs: 16961 / % possible obs: 96.3 % / Observed criterion σ(I): -2 / Redundancy: 3.8 % / Biso Wilson estimate: 45.2 Å2 / Limit h max: 29 / Limit h min: 0 / Limit k max: 56 / Limit k min: 0 / Limit l max: 36 / Limit l min: 0 / Observed criterion F max: 836060.11 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.058 / Rsym value: 0.043 / Net I/σ(I): 30
Reflection shellResolution: 2.21→2.26 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 1.9 / Num. unique all: 719 / Rsym value: 0.456 / % possible all: 85.2
Reflection
*PLUS
Highest resolution: 2.22 Å / Lowest resolution: 35 Å / Redundancy: 4.11 %
Reflection shell
*PLUS
Highest resolution: 2.22 Å / % possible obs: 85.2 % / Mean I/σ(I) obs: 1.87

-
Processing

Software
NameVersionClassificationNB
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1NPP

1npp


Resolution: 2.21→29.19 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 749 4.8 %random
Rwork0.236 ---
all-16961 --
obs-15493 87.7 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 61.3083 Å2 / ksol: 0.333095 e/Å3
Displacement parametersBiso max: 133.8 Å2 / Biso mean: 62.97 Å2 / Biso min: 25.8 Å2
Baniso -1Baniso -2Baniso -3
1-21.02 Å20 Å20 Å2
2---12.95 Å20 Å2
3----8.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.35 Å
Luzzati d res low-30 Å
Luzzati sigma a0.52 Å0.5 Å
Luzzati d res high-2.21
Refinement stepCycle: LAST / Resolution: 2.21→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1917 0 0 144 2061
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.21-2.310.419592.70.41813660.0552148142566.3
2.31-2.430.368853.90.36716260.042204171177.6
2.43-2.580.329904.20.32617320.0352162182284.3
2.58-2.780.2938740.28918430.0312201193087.7
2.78-3.060.2621034.70.26119300.0262205203392.2
3.06-3.50.24611050.24920170.0232215212796
3.5-4.410.2111155.10.21420720.022236218797.8
4.41-29.190.1971004.30.19321580.022322225897.2
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.22 Å / Lowest resolution: 35 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

+
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