[English] 日本語
Yorodumi
- PDB-1z43: Crystal structure of 7S.S SRP RNA of M. jannaschii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1z43
TitleCrystal structure of 7S.S SRP RNA of M. jannaschii
ComponentsRNA (101-MER)
KeywordsRNA / tetra-loop
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHainzl, T. / Huang, S. / Sauer-Eriksson, A.E.
Citation
Journal: Rna / Year: 2005
Title: Structural insights into SRP RNA: An induced fit mechanism for SRP assembly
Authors: Hainzl, T. / Huang, S. / Sauer-Eriksson, A.E.
#1: Journal: Nature / Year: 2002
Title: Structure of the SRP19 RNA complex and implications for signal recognition particle assembly
Authors: Hainzl, T. / Huang, S. / Sauer-Eriksson, A.E.
History
DepositionMar 15, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA (101-MER)


Theoretical massNumber of molelcules
Total (without water)32,7701
Polymers32,7701
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.110, 62.110, 247.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: RNA chain RNA (101-MER) / 7S.S SRP RNA / 7S SRP RNA


Mass: 32769.543 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 3.64 Å3/Da / Density % sol: 66.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 400, Tris buffer, sodium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2Tris buffer11
3sodium citrate11
4H2O11
5PEG 40012
6Tris buffer12
7sodium citrate12
8H2O12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.081 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.081 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 15814 / Num. obs: 15645 / % possible obs: 98.9 % / Observed criterion σ(F): 78570 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.7 Å / Num. unique all: 1632 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LNG

1lng


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 18.786 / SU ML: 0.364 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.43 / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29616 783 5 %RANDOM
Rwork0.2531 ---
obs0.2552 14857 98.9 %-
all-15640 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.874 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å20 Å20 Å2
2--2.44 Å20 Å2
3----4.88 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2169 0 139 2308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212427
X-RAY DIFFRACTIONr_bond_other_d0.0020.02819
X-RAY DIFFRACTIONr_angle_refined_deg3.22633787
X-RAY DIFFRACTIONr_angle_other_deg2.02432141
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021061
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.320.31220
X-RAY DIFFRACTIONr_nbd_other0.360.31418
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0260.58
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2460.5208
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1280.510
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.321
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1590.38
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2740.57
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it2.0532427
X-RAY DIFFRACTIONr_scangle_it3.0074.53787
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.37 40
Rwork0.458 1051
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)
16.1014-2.55421.34661.9712-2.333.2089-0.01660.02380.05070.0454-0.13580.0555-0.2436-0.03540.15240.3863-0.00110.08610.3913-0.04440.318646.6659-6.8158113.3783
23.0243-1.07890.81671.1813-2.31224.25370.14380.36270.16840.0379-0.20620.12960.06070.62350.06240.3539-0.04430.04110.39350.05320.439238.73912.717896.9195
310.71752.42345.20984.393-1.71021.9753-0.08680.320.6706-0.42780.56030.81080.1144-0.6856-0.47360.30490.01770.20390.77760.11610.293520.01995.0654102.324
4-2.0784-1.42142.85852.4155-5.60274.67050.3216-0.5064-0.3469-0.96610.20970.1561.3979-0.5524-0.53120.552-0.1139-0.02250.83470.15730.65679.26475.991581.3993
54.9218-2.45012.36532.1865-2.7261.16080.0493-0.0781-0.2088-0.10920.03120.1426-0.0954-0.2693-0.08040.32490.03530.05670.4425-0.01910.433224.017516.755874.238
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A138 - 147
2X-RAY DIFFRACTION1A232 - 238
3X-RAY DIFFRACTION2A182 - 197
4X-RAY DIFFRACTION2A224 - 231
5X-RAY DIFFRACTION3A148 - 152
6X-RAY DIFFRACTION3A178 - 181
7X-RAY DIFFRACTION4A153 - 177
8X-RAY DIFFRACTION5A198 - 223

+
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