[English] 日本語
Yorodumi
- PDB-5k71: apo Dbr1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5k71
Titleapo Dbr1
ComponentsRNA lariat debranching enzyme, putative
KeywordsHYDROLASE / metalloenzyme / apo-enzyme
Function / homology
Function and homology information


RNA lariat debranching enzyme activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / RNA splicing, via transesterification reactions / mRNA splicing, via spliceosome / manganese ion binding / iron ion binding / perinuclear region of cytoplasm / RNA binding / zinc ion binding / nucleus
Similarity search - Function
Lariat debranching enzyme, N-terminal metallophosphatase domain / : / Dbr1, C-terminal domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
Lariat debranching enzyme
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.57 Å
AuthorsClark, N.E. / Taylor, A.B. / Hart, P.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: The RNA lariat debranching enzyme Dbr1: metal dependence and branched RNA co-crystal structures
Authors: Clark, N.E. / Katolik, A. / Roberts, K. / Taylor, A.B. / Holloway, S.P. / Schuermann, J.P. / Montemayor, E.J. / Stevens, S.W. / Fitzpatrick, P.F. / Damha, M.J. / Hart, P.J.
History
DepositionMay 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support / Item: _citation.journal_id_CSD
Revision 1.2Sep 27, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA lariat debranching enzyme, putative
B: RNA lariat debranching enzyme, putative
C: RNA lariat debranching enzyme, putative
D: RNA lariat debranching enzyme, putative
E: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,60321
Polymers206,0665
Non-polymers1,53716
Water6,756375
1
A: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5014
Polymers41,2131
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5014
Polymers41,2131
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6946
Polymers41,2131
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5014
Polymers41,2131
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: RNA lariat debranching enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4053
Polymers41,2131
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.110, 142.163, 214.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
RNA lariat debranching enzyme, putative


Mass: 41213.266 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_062730 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: C4M1P9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.7 Å3/Da / Density % sol: 54.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, lithium sulfate, glycerol, bis-tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.57→107.15 Å / Num. obs: 134191 / % possible obs: 99.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.6
Reflection shellResolution: 2.57→2.63 Å / Redundancy: 5 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.6 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4PEF

4pef


Resolution: 2.57→107.15 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2422 6717 5.01 %
Rwork0.1943 --
obs0.1967 134191 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.57→107.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14285 0 80 375 14740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314763
X-RAY DIFFRACTIONf_angle_d0.6419968
X-RAY DIFFRACTIONf_dihedral_angle_d17.2255457
X-RAY DIFFRACTIONf_chiral_restr0.0472092
X-RAY DIFFRACTIONf_plane_restr0.0042497
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)
13.09630.44480.18552.666-0.01571.5574-0.0519-0.2442-0.04550.03780.16-0.0279-0.1755-0.2417-0.1150.28720.0627-0.05590.3746-0.01380.31570.6899-38.8382-24.0311
22.77220.16290.66522.3875-0.28641.6010.15890.08610.312-0.0352-0.12280.0023-0.00890.1581-0.04110.3148-0.0536-0.04720.31740.08370.31534.6168-68.7038-19.546
31.4407-0.2169-0.39542.52640.34061.3162-0.03270.0216-0.09950.1605-0.111-0.14340.12490.04970.14310.4075-0.0406-0.1270.26780.04010.310353.3191-88.59449.6834
42.06010.0811-1.7471.74910.41783.51410.1489-0.52740.01110.21420.08510.0351-0.23530.3398-0.17880.31-0.12110.02610.56230.00030.380141.9668-82.17-65.5289
51.7539-0.34350.72633.81-1.18793.1272-0.11970.18520.0656-0.5093-0.04090.3680.3713-0.18960.17150.3812-0.0894-0.02410.3621-0.00240.31428.1793-96.047-43.96
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 5 through 353)
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 353)
3X-RAY DIFFRACTION3(chain 'C' and resid 5 through 353)
4X-RAY DIFFRACTION4(chain 'D' and resid 5 through 353)
5X-RAY DIFFRACTION5(chain 'E' and resid 5 through 353)

+
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://pdbjlvh1.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