[English] 日本語
Yorodumi
- PDB-1hus: RIBOSOMAL PROTEIN S7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hus
TitleRIBOSOMAL PROTEIN S7
ComponentsRIBOSOMAL PROTEIN S7
KeywordsRIBOSOMAL PROTEIN / RNA-BINDING PROTEIN / DECODING CENTER
Function / homology
Function and homology information


small ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation
Similarity search - Function
Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / Ribosomal protein S7p/S5e / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
30S ribosomal protein S7
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD WITH SE-MET MUTANT / Resolution: 2.5 Å
AuthorsHosaka, H. / Nakagawa, A. / Tanaka, I.
Citation
Journal: Structure / Year: 1997
Title: Ribosomal protein S7: a new RNA-binding motif with structural similarities to a DNA architectural factor.
Authors: Hosaka, H. / Nakagawa, A. / Tanaka, I. / Harada, N. / Sano, K. / Kimura, M. / Yao, M. / Wakatsuki, S.
#1: Journal: J.Struct.Biol. / Year: 1997
Title: Crystallization and Preliminary X-Ray Crystallographic Study of the Ribosomal Protein S7 from Bacillus Stearothermophilus
Authors: Harada, N. / Sano, K. / Kimura, M. / Hosaka, H. / Nakagawa, A. / Tanaka, I.
History
DepositionAug 8, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RIBOSOMAL PROTEIN S7


Theoretical massNumber of molelcules
Total (without water)18,2301
Polymers18,2301
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.400, 131.020, 29.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein RIBOSOMAL PROTEIN S7


Mass: 18230.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Cell line: BL21 / Gene: S7 / Plasmid: BL21 / Gene (production host): S7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) LYSS / References: UniProt: P22744
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growpH: 8.2
Details: PROTEIN WAS CRYSTALLIZED FROM 0.1M NA HEPES BUFFER(PH8.2) WITH 4%(V/V) 2-PROPANOL AND 2.0M AMMONIUM SULFATE.
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium HEPES11
24 %(v/v)2-propanol11
32.0 Mammonium sulfate11

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.90007
DetectorType: PRINCETON 2K / Detector: CCD / Date: Mar 1, 1997 / Details: COLLIMATING AND FOCUSING MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90007 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 7586 / % possible obs: 97.6 % / Observed criterion σ(I): 18.7 / Redundancy: 2.8 % / Biso Wilson estimate: 33.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 20.3
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 5.8 / % possible all: 92.9
Reflection
*PLUS
Num. measured all: 53236
Reflection shell
*PLUS
% possible obs: 92.9 %

-
Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MAD WITH SE-MET MUTANT / Resolution: 2.5→8 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: REFMAC (G.N.MURSHUDOV ET AL.) WAS ALSO USED DURING THE REFINEMENT CYCLE. PARAMETERS OF SE-MET WAS DERIVED FROM THOSE OF METHIONINE.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 715 9.8 %RANDOM
Rwork0.216 ---
obs0.216 7305 98 %-
Displacement parametersBiso mean: 33.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1120 0 0 25 1145
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.02
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_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.12
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it8.231.5
X-RAY DIFFRACTIONx_mcangle_it10.572
X-RAY DIFFRACTIONx_scbond_it11.452
X-RAY DIFFRACTIONx_scangle_it16.272.5
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.339 81 9.5 %
Rwork0.353 769 -
obs--93.3 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.12

+
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