[English] 日本語
Yorodumi
- PDB-3qrr: Structure of Thermus Thermophilus Cse3 bound to an RNA representi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qrr
TitleStructure of Thermus Thermophilus Cse3 bound to an RNA representing a product complex
Components
  • Putative uncharacterized protein TTHB192
  • RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP*GP*GP*(23G))-3')
KeywordsRNA BINDING PROTEIN/RNA / protein-RNA complex / RAMP domain / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding
Similarity search - Function
Crispr-associated protein; domain 1 / Crispr-associated protein; domain 2 / CRISPR-associated protein Cse3 / CRISPR associated protein / CRISPR_assoc / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / CRISPR-associated endoribonuclease Cse3
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.099 Å
AuthorsSchellenberg, M.J. / Gesner, E.G. / Garside, E.L. / MacMillan, A.M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Recognition and maturation of effector RNAs in a CRISPR interference pathway.
Authors: Gesner, E.M. / Schellenberg, M.J. / Garside, E.L. / George, M.M. / Macmillan, A.M.
History
DepositionFeb 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein TTHB192
B: RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP*GP*GP*(23G))-3')


Theoretical massNumber of molelcules
Total (without water)35,8602
Polymers35,8602
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative uncharacterized protein TTHB192
B: RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP*GP*GP*(23G))-3')

A: Putative uncharacterized protein TTHB192
B: RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP*GP*GP*(23G))-3')


Theoretical massNumber of molelcules
Total (without water)71,7204
Polymers71,7204
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area6820 Å2
ΔGint-32 kcal/mol
Surface area25360 Å2
MethodPISA
3
A: Putative uncharacterized protein TTHB192

B: RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP*GP*GP*(23G))-3')


Theoretical massNumber of molelcules
Total (without water)35,8602
Polymers35,8602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
Buried area1530 Å2
ΔGint-13 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.170, 68.747, 155.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Putative uncharacterized protein TTHB192


Mass: 30002.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: TTHB1192, TTHB192 / Plasmid: PET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q53WG9
#2: RNA chain RNA (5'-R(*GP*UP*CP*CP*CP*CP*AP*CP*GP*CP*GP*UP*GP*UP*GP*GP*GP*(23G))-3')


Mass: 5857.448 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized RNA

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 3350, 100mM KOAc, 1mM spermidine, pH 7.5, vapour diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.11588 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 11, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 3.099→46.111 Å / Num. all: 6367 / Num. obs: 6268 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.099→3.179 Å / % possible all: 98.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
SCALEPACKdata scaling
REFMAC5.5.0110phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.099→46.111 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.818 / WRfactor Rfree: 0.2688 / WRfactor Rwork: 0.2146 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8387 / SU B: 39.225 / SU ML: 0.348 / SU R Cruickshank DPI: 0.4553 / SU Rfree: 0.552 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.552 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3003 288 4.6 %RANDOM
Rwork0.2454 ---
obs0.2479 5979 98.41 %-
all-6076 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.16 Å2 / Biso mean: 55.434 Å2 / Biso min: 13.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2---1.26 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 3.099→46.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 386 0 0 2017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222098
X-RAY DIFFRACTIONr_angle_refined_deg0.6572.2262928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2835202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87221.275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39515293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8831525
X-RAY DIFFRACTIONr_chiral_restr0.0340.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211455
X-RAY DIFFRACTIONr_mcbond_it0.1421.51021
X-RAY DIFFRACTIONr_mcangle_it0.25921639
X-RAY DIFFRACTIONr_scbond_it0.2331077
X-RAY DIFFRACTIONr_scangle_it0.394.51289
LS refinement shellResolution: 3.099→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.489 18 -
Rwork0.315 421 -
all-439 -
obs--98.87 %
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)
13.84751.20450.4273.04220.87541.91670.0915-0.07950.00690.1642-0.10350.0043-0.0783-0.05040.0120.05440.0323-0.01250.1570.00550.3369-20.184-12.526-26.944
22.4125-0.0423.13720.0449-0.10154.38040.0137-0.1858-0.0636-0.03690.1552-0.03110.3189-0.241-0.16890.36970.0101-0.1970.6031-0.01330.37-1.883-14.8430.678
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 219
2X-RAY DIFFRACTION2B4 - 21

+
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