[English] 日本語
Yorodumi
- PDB-1hmh: THREE-DIMENSIONAL STRUCTURE OF A HAMMERHEAD RIBOZYME -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hmh
TitleTHREE-DIMENSIONAL STRUCTURE OF A HAMMERHEAD RIBOZYME
Components
  • HAMMERHEAD RIBOZYME-DNA STRAND
  • HAMMERHEAD RIBOZYME-RNA STRAND
KeywordsRIBOZYME / DNA-RNA HAMMERHEAD RIBOZYME / LOOP
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsPley, H.W. / Flaherty, K.M. / McKay, D.B.
Citation
Journal: Nature / Year: 1994
Title: Three-dimensional structure of a hammerhead ribozyme.
Authors: Pley, H.W. / Flaherty, K.M. / McKay, D.B.
#1: Journal: Nature / Year: 1994
Title: Model for an RNA Tertiary Interaction from the Structure of an Intermolecular Complex Between a GAAA Tetraloop and an RNA Helix
Authors: Pley, H.W. / Flaherty, K.M. / McKay, D.B.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: The Crystal Structure of an All-RNA Hammerhead Ribozyme: a Proposed Mechanism for RNA Catalytic Cleavage
Authors: Scott, W.G. / Finch, J.T. / Klug, A.
#3: Journal: J.Biol.Chem. / Year: 1993
Title: Crystals of a Hammerhead Ribozyme
Authors: Pley, H.W. / Lindes, D.S. / Deluca-Flaherty, C. / McKay, D.B.
History
DepositionJun 6, 1995Deposition site: BNL / Processing site: NDB
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HAMMERHEAD RIBOZYME-RNA STRAND
B: HAMMERHEAD RIBOZYME-DNA STRAND
C: HAMMERHEAD RIBOZYME-RNA STRAND
D: HAMMERHEAD RIBOZYME-DNA STRAND
E: HAMMERHEAD RIBOZYME-RNA STRAND
F: HAMMERHEAD RIBOZYME-DNA STRAND


Theoretical massNumber of molelcules
Total (without water)44,9986
Polymers44,9986
Non-polymers00
Water00
1
A: HAMMERHEAD RIBOZYME-RNA STRAND
B: HAMMERHEAD RIBOZYME-DNA STRAND


Theoretical massNumber of molelcules
Total (without water)14,9992
Polymers14,9992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: HAMMERHEAD RIBOZYME-RNA STRAND
D: HAMMERHEAD RIBOZYME-DNA STRAND


Theoretical massNumber of molelcules
Total (without water)14,9992
Polymers14,9992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: HAMMERHEAD RIBOZYME-RNA STRAND
F: HAMMERHEAD RIBOZYME-DNA STRAND


Theoretical massNumber of molelcules
Total (without water)14,9992
Polymers14,9992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.740, 89.740, 185.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: RNA chain HAMMERHEAD RIBOZYME-RNA STRAND


Mass: 11030.680 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
#2: DNA chain HAMMERHEAD RIBOZYME-DNA STRAND


Mass: 3968.573 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.8 Å3/Da / Density % sol: 74.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NH4 SULFATE11
3MGCL211
4SPERMINE11
5CACODYLATE11
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
210 mMsodium cacodylate1drop
31.9-2.2 Mammonium sulfate1reservoiror 1.5-2.2 M LiSO4
40-100 mM1reservoirMgCl2
50-2 mMspermine1reservoir
610 mMcacodylate1reservoir

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.6 Å / Num. all: 135854 / Num. obs: 26816

-
Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.6→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.305 --
Rwork0.257 --
obs0.257 24660 95.6 %
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2994 0 0 2994
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_deg1.35
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d10.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.95
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
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg10.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.95

+
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