[English] 日本語
Yorodumi
- PDB-488d: CATALYTIC RNA ENZYME-PRODUCT COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 488d
TitleCATALYTIC RNA ENZYME-PRODUCT COMPLEX
Components
  • FIRST RNA FRAGMENT OF CLEAVED SUBSTRATE
  • RNA RIBOZYME STRAND
  • SECOND RNA FRAGMENT OF CLEAVED SUBSTRATE
  • UNCLEAVED RNA SUBSTRATE
KeywordsRNA / CATALYTIC RNA / RIBOZYME / ENZYME-PRODUCT COMPLEX / CRYSTAL LATTICE TRAPPING
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsMurray, J.B. / Szoke, H. / Szoke, A. / Scott, W.G.
CitationJournal: Mol.Cell / Year: 2000
Title: Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction.
Authors: Murray, J.B. / Szoke, H. / Szoke, A. / Scott, W.G.
History
DepositionFeb 25, 2000Deposition site: NDB / Processing site: NDB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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
A: RNA RIBOZYME STRAND
B: FIRST RNA FRAGMENT OF CLEAVED SUBSTRATE
C: SECOND RNA FRAGMENT OF CLEAVED SUBSTRATE
D: UNCLEAVED RNA SUBSTRATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,12612
Polymers21,2274
Non-polymers8998
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.503, 65.503, 136.484
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

-
Components

#1: RNA chain RNA RIBOZYME STRAND


Mass: 5170.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 16-MER
#2: RNA chain FIRST RNA FRAGMENT OF CLEAVED SUBSTRATE


Mass: 6507.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 20-MER, 3'-END CYCLIC PHOSPHATE
#3: RNA chain SECOND RNA FRAGMENT OF CLEAVED SUBSTRATE


Mass: 1529.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5-MER
#4: RNA chain UNCLEAVED RNA SUBSTRATE


Mass: 8019.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 25-MER
#5: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 78 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5 / Details: pH 5.00, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMribozyme1drop
250 mM1dropNaOAc
31.8 M1dropLi2SO4
450 mM1reservoirNaOAc
51.8 M1reservoirLi2SO4
61.0 mMEDTA1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.2
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Oct 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 3.1→24.6 Å / Num. all: 6553 / Num. obs: 6553 / % possible obs: 95.5 % / Redundancy: 1.7 % / Rsym value: 0.104
Reflection shellResolution: 3.1→3.4 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.275 / % possible all: 91.3
Reflection
*PLUS
Num. measured all: 10825
Reflection shell
*PLUS
% possible obs: 91.3 % / Num. unique obs: 834 / Num. measured obs: 6253 / Mean I/σ(I) obs: 2.4

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementResolution: 3.1→24.6 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE CRYSTAL IS A MIXTURE OF 40% CLEAVED HAMMERHEAD RNA AND 60% UNCLEAVED HAMMERHEAD RNA. THE OCCUPANCY OF THE ENZYME STRAND AND METALS PRESENT ARE SET TO 1.0 AND THE CHAIN IS LABELLED 'A'. ...Details: THE CRYSTAL IS A MIXTURE OF 40% CLEAVED HAMMERHEAD RNA AND 60% UNCLEAVED HAMMERHEAD RNA. THE OCCUPANCY OF THE ENZYME STRAND AND METALS PRESENT ARE SET TO 1.0 AND THE CHAIN IS LABELLED 'A'. THE OCCUPANCY OF THE SUBSTRATE STRAND IS SET TO 0.6 AND LABELLED AS CHAIN 'D'. THE OCCUPANCY OF THE PRODUCT STRAND (OR CLEAVED STRAND) IS 0.4 AND IS LABELLED 'B' AND 'C'. THE RELATIVE OCCUPANCIES WERE DETERMINED BY HPLC. A SECOND CRYSTAL WHOSE STRUCTURE IS ESSENTIALLY IDENTICAL WAS ALSO ANALYZED, IN WHICH 60% OF THE RNA HAD CLEAVED. HOWEVER, THE QUALITY OF THE DATA FOR THE SUBMITTED CRYSTAL STRUCTURE IS SOMEWHAT HIGHER.
RfactorNum. reflection% reflectionSelection details
Rfree0.301 618 9.4 %random
Rwork0.258 ---
obs0.258 6553 95.5 %-
all-6553 --
Refinement stepCycle: LAST / Resolution: 3.1→24.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1404 8 0 1412
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.89
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg35.2
X-RAY DIFFRACTIONx_improper_angle_deg1.3

+
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