[English] 日本語
Yorodumi
- PDB-1ztt: Netropsin bound to d(CTTAATTCGAATTAAG) in complex with MMLV RT ca... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ztt
TitleNetropsin bound to d(CTTAATTCGAATTAAG) in complex with MMLV RT catalytic fragment
Components
  • 5'-D(*CP*TP*TP*AP*AP*TP*TP*C)-3'
  • 5'-D(P*GP*AP*AP*TP*TP*AP*AP*G)-3'
  • Reverse transcriptase
KeywordsTransferase/DNA / Netropsin / MMLV-RT / Drug-DNA complex / Protein-DNA complex / Transferase-DNA COMPLEX
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Antitermination protein Q / Antitermination protein Q superfamily / Antitermination protein / Heat shock protein DnaJ, cysteine-rich domain superfamily / HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Alpha-Beta Plaits / Roll ...Antitermination protein Q / Antitermination protein Q superfamily / Antitermination protein / Heat shock protein DnaJ, cysteine-rich domain superfamily / HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NETROPSIN / DNA / Antitermination protein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsGoodwin, K.D. / Long, E.C. / Georgiadis, M.M.
CitationJournal: Nucleic Acids Res. / Year: 2005
Title: A host-guest approach for determining drug-DNA interactions: an example using netropsin.
Authors: Goodwin, K.D. / Long, E.C. / Georgiadis, M.M.
History
DepositionMay 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 5'-D(*CP*TP*TP*AP*AP*TP*TP*C)-3'
G: 5'-D(P*GP*AP*AP*TP*TP*AP*AP*G)-3'
A: Reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2164
Polymers33,7863
Non-polymers4301
Water5,080282
1
B: 5'-D(*CP*TP*TP*AP*AP*TP*TP*C)-3'
G: 5'-D(P*GP*AP*AP*TP*TP*AP*AP*G)-3'
A: Reverse transcriptase
hetero molecules

B: 5'-D(*CP*TP*TP*AP*AP*TP*TP*C)-3'
G: 5'-D(P*GP*AP*AP*TP*TP*AP*AP*G)-3'
A: Reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4328
Polymers67,5716
Non-polymers8612
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Unit cell
Length a, b, c (Å)54.569, 145.611, 46.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly consists of two protein molecules bound to the 16 base pair DNA duplex with two netropsin molecules bound.

-
Components

#1: DNA chain 5'-D(*CP*TP*TP*AP*AP*TP*TP*C)-3'


Mass: 2376.591 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*GP*AP*AP*TP*TP*AP*AP*G)-3'


Mass: 2474.667 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Reverse transcriptase / RT


Mass: 28934.287 Da / Num. of mol.: 1 / Fragment: RT catalytic fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus / Genus: Gammaretrovirus / Species: Murine leukemia virus / Gene: POL / Production host: Escherichia coli (E. coli) / References: UniProt: P03355, RNA-directed DNA polymerase
#4: Chemical ChemComp-NT / NETROPSIN


Mass: 430.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26N10O3 / Comment: antibiotic, antivirus*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 4000, magnesium acetate, ADA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2magnesium acetate11
3ADA11
4H2O11
5PEG 400012
6magnesium acetate12
7ADA12
8H2O12

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 29, 2004
RadiationMonochromator: Osmic Confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 32157 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.85→1.92 Å / % possible all: 99.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→35.5 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.246 1536 Random
Rwork0.22 --
all0.23 32374 -
obs0.22 31059 -
Refinement stepCycle: LAST / Resolution: 1.85→35.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 325 31 282 2679
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004966
X-RAY DIFFRACTIONc_angle_deg1.24301
X-RAY DIFFRACTIONc_mcbond_it1.5761.5
X-RAY DIFFRACTIONc_scbond_it1.9592
X-RAY DIFFRACTIONc_mcangle_it2.5892
X-RAY DIFFRACTIONc_scangle_it3.0352.5

+
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