[English] 日本語
Yorodumi
- PDB-1gid: CRYSTAL STRUCTURE OF A GROUP I RIBOZYME DOMAIN: PRINCIPLES OF RNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gid
TitleCRYSTAL STRUCTURE OF A GROUP I RIBOZYME DOMAIN: PRINCIPLES OF RNA PACKING
ComponentsP4-P6 RNA RIBOZYME DOMAIN
KeywordsRIBOZYME / RNA / P4-P6 RIBOZYME DOMAIN OF THE TETRAHYMENA GROUP I INTRON
Function / homologyCOBALT HEXAMMINE(III) / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD-SIR / Resolution: 2.5 Å
AuthorsCate, J.H. / Gooding, A.R. / Podell, E. / Zhou, K. / Golden, B.L. / Kundrot, C.E. / Cech, T.R. / Doudna, J.A.
Citation
Journal: Science / Year: 1996
Title: Crystal structure of a group I ribozyme domain: principles of RNA packing.
Authors: Cate, J.H. / Gooding, A.R. / Podell, E. / Zhou, K. / Golden, B.L. / Kundrot, C.E. / Cech, T.R. / Doudna, J.A.
#1: Journal: Science / Year: 1996
Title: RNA Tertiary Structure Mediation by Adenosine
Authors: Cate, J.H. / Gooding, A.R. / Podell, E. / Zhou, K. / Golden, B.L. / Szewczak, A.A. / Kundrot, C.E. / Cech, T.R. / Doudna, J.A.
#2: Journal: Structure / Year: 1996
Title: Metal-Binding Sites in the Major Groove of a Large Ribozyme Domain
Authors: Cate, J.H. / Doudna, J.A.
History
DepositionAug 22, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Dec 31, 1996Provider: 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE REFERENCE: MURPHY, F.L., CECH, T.R. BIOCHEMISTRY 32, 5291 (1993).

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: P4-P6 RNA RIBOZYME DOMAIN
B: P4-P6 RNA RIBOZYME DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,33030
Polymers102,1032
Non-polymers1,22828
Water1086
1
A: P4-P6 RNA RIBOZYME DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,66515
Polymers51,0511
Non-polymers61414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: P4-P6 RNA RIBOZYME DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,66515
Polymers51,0511
Non-polymers61414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.800, 128.700, 145.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: RNA chain P4-P6 RNA RIBOZYME DOMAIN


Mass: 51051.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: T7 TRANSCRIPT / Source: (natural) synthetic construct (others)
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CoH18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.3 Å3/Da / Density % sol: 71 %
Crystal growMethod: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2K CACODYLATE11
3MGCL211
4SPERMINE11
5[CO(NH3)6]CL311
6WATER12
7MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
160 mMpotassium cacodylate1reservoir
230 mMmagnesium chloride1reservoir
30.3 mMspermine1reservoir
40.2-1.0 mMcobalt hexammine chloride1reservoir
5methylpentanediol1reservoir
61
71

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorDetector: CCD / Date: Dec 30, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→18 Å / Num. obs: 36401 / % possible obs: 73 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rsym value: 0.043 / Net I/σ(I): 23.7
Reflection shellResolution: 2.77→2.86 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.264 / % possible all: 80.2

-
Processing

Software
NameVersionClassification
MAD-SIRmodel building
X-PLOR3.843refinement
DENZOdata reduction
CCP4data scaling
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD-SIR / Resolution: 2.5→8 Å / Cross valid method: FREE R / σ(F): 2
Details: NUCLEIC ACID RNA-DNA PARAMETER FILE: G. PARKINSON,ET AL. (1996) ACTA CRYST. D52, 57-64
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1788 5.4 %RANDOM
Rwork0.242 ---
obs0.242 35100 73.5 %-
Displacement parametersBiso mean: 45 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 6766 52 6 6824
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_deg1.27
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d13.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.78
X-RAY DIFFRACTIONx_mcangle_it5.87
X-RAY DIFFRACTIONx_scbond_it2.98
X-RAY DIFFRACTIONx_scangle_it4.59
Refine LS restraints NCSNCS model details: 14 GROUPS
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.51 72 5 %
Rwork0.398 1368 -
obs--60.3 %
Xplor fileSerial no: 2 / Param file: DNA-RNA-MULTI-ENDO.PARAM / Topol file: DNA-RNA-MULTI-ENDO.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg13.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2
X-RAY DIFFRACTIONx_mcbond_it3.78
X-RAY DIFFRACTIONx_scbond_it2.98
X-RAY DIFFRACTIONx_mcangle_it5.87
X-RAY DIFFRACTIONx_scangle_it4.59
LS refinement shell
*PLUS
Rfactor Rfree: 0.51 / % reflection Rfree: 5 % / Total num. of bins used: 20

+
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