[English] 日本語
Yorodumi
- PDB-7c43: The crystal structure of Trypanosoma brucei RNase D : AMP complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c43
TitleThe crystal structure of Trypanosoma brucei RNase D : AMP complex
ComponentsCCHC-type domain-containing protein
KeywordsHYDROLASE / Trypanosoma brucei / RNase D / guide RNA degradation / RNA BINDING PROTEIN / AMP
Function / homology
Function and homology information


PET complex / nucleobase-containing compound metabolic process / 3'-5'-RNA exonuclease activity / nucleic acid binding / nucleotide binding / mitochondrion / zinc ion binding
Similarity search - Function
: / 3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / : / CCHC-type domain-containing protein
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsGao, Y.Q. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019FY101500 China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural basis for guide RNA trimming by RNase D ribonuclease in Trypanosoma brucei.
Authors: Gao, Y. / Liu, H. / Zhang, C. / Su, S. / Chen, Y. / Chen, X. / Li, Y. / Shao, Z. / Zhang, Y. / Shao, Q. / Li, J. / Huang, Z. / Ma, J. / Gan, J.
History
DepositionMay 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CCHC-type domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5746
Polymers38,9861
Non-polymers5885
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-18 kcal/mol
Surface area15070 Å2
Unit cell
Length a, b, c (Å)49.730, 77.730, 99.301
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CCHC-type domain-containing protein / RNase D


Mass: 38986.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Strain: 927/4 GUTat10.1 / Gene: Tb09.211.3670 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38DE2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Bis-Tris pH 5.5, 30% PEG 3350

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→61.21 Å / Num. obs: 17294 / % possible obs: 97.4 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.023 / Rrim(I) all: 0.074 / Χ2: 0.91 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.384.80.27915940.8850.1220.3070.89991.6
2.38-2.485.20.27216520.9210.1170.2980.88995.4
2.48-2.596.30.2416830.9470.0950.2590.91596.6
2.59-2.737.40.21816930.970.080.2330.90197.5
2.73-2.98.20.16417150.9890.0570.1740.91998.3
2.9-3.128.80.11817500.9940.040.1250.93998.4
3.12-3.439.30.08517370.9970.0270.0890.90798.5
3.43-3.9311.30.06417690.9980.0190.0670.93899.2
3.93-4.9510.90.05118020.9980.0160.0540.85799.5
4.95-3011.20.05318990.9980.0160.0560.92299

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→61.21 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.902 / SU B: 6.586 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.31 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 808 5.1 %RANDOM
Rwork0.1999 ---
obs0.2021 15127 89.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.72 Å2 / Biso mean: 32.742 Å2 / Biso min: 14.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2---0.06 Å2-0 Å2
3----0.69 Å2
Refinement stepCycle: final / Resolution: 2.3→61.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 27 26 2345
Biso mean--42.38 29.18 -
Num. residues----295
LS refinement shellResolution: 2.3→2.358 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.23 36 -
Rwork0.233 726 -
obs--59.25 %

+
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