[English] 日本語
Yorodumi
- PDB-1ln4: CRYSTAL STRUCTURE OF E. COLI YHBY -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ln4
TitleCRYSTAL STRUCTURE OF E. COLI YHBY
ComponentsHypothetical protein yhbY
KeywordsRNA BINDING PROTEIN / PUTATIVE RNA-BINDING PROTEIN / PUTATIVE TRANSLATION FACTOR
Function / homology
Function and homology information


rRNA 5'-end processing / preribosome binding / ribosomal large subunit assembly / ribosomal small subunit assembly / RNA binding / cytosol
Similarity search - Function
YhbY-like / RNA-binding, CRM domain / RNA-binding protein YhbY / YhbY-like superfamily / CRS1 / YhbY (CRM) domain / CRM domain profile. / CRS1_YhbY / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA-binding protein YhbY / RNA-binding protein YhbY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsOstheimer, G.J. / Barkan, A. / Matthews, B.W.
CitationJournal: Structure / Year: 2002
Title: Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins
Authors: Ostheimer, G.J. / Barkan, A. / Matthews, B.W.
History
DepositionMay 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein yhbY


Theoretical massNumber of molelcules
Total (without water)11,7181
Polymers11,7181
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.324, 57.324, 70.895
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Hypothetical protein yhbY / yhbY


Mass: 11717.667 Da / Num. of mol.: 1 / Mutation: N2D,R97L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YHBY / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Gold / References: UniProt: P42550, UniProt: P0AGK4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.87 Å3/Da / Density % sol: 57.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 200, sodium chloride, tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
150 mM1dropNaCl
210 mMTris1droppH7.0
30.1 mMEDTA1drop
45 mMdithiothreitol1drop
510 mg/mlprotein1drop
645 %(v/v)PEG2001reservoir
7100 mMTris1reservoirpH8.5
8100 mM1reservoirNaCl

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.210.9611,0.9793,0.9792
SYNCHROTRONALS 5.0.121
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 28, 2001
ADSC QUANTUM 42CCDJun 28, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DOUBLE CRYSTAL SIMADMx-ray1
2SINGLE CRYSTAL SI CYLINDRICALLY BENTSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.96111
20.97931
30.97921
411
ReflectionResolution: 1.5→20 Å / Num. all: 22101 / Num. obs: 22089 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 4.5
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 4.5 / Num. unique all: 3170 / Rsym value: 0.139 / % possible all: 99.9
Reflection
*PLUS
Num. obs: 22061 / % possible obs: 100 %
Reflection shell
*PLUS
% possible obs: 99.9 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SOLVEphasing
SCALAdata scaling
TNT5Frefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.5→20 Å / Isotropic thermal model: TNT BCORREL V1.0 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT GEOMETRY V1.0
Details: PHASES WERE DETERMINED USING A 3-WAVELENGTH MAD DATASET COLLECTED ON A SINGLE CRYSTAL. THE STRUCTURE WAS REFINED AGAINST AN ADDITIONAL MONOCHROMATIC DATASET THAT WAS COLLECTED USING THE SAME CRYSTAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1119 5 %random
Rwork0.192 ---
all0.193 22103 --
obs0.193 22061 100 %-
Solvent computationBsol: 207.501 Å2 / ksol: 0.82848 e/Å3
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms769 0 0 107 876
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0157770.4
X-RAY DIFFRACTIONt_angle_deg2.76610440.5
X-RAY DIFFRACTIONt_dihedral_angle_d16.1254870
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.004192
X-RAY DIFFRACTIONt_gen_planes0.0111064
X-RAY DIFFRACTIONt_it6.367770.1
X-RAY DIFFRACTIONt_nbd0.0181110
Refinement
*PLUS
Num. reflection obs: 21928 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_angle_deg2.8
X-RAY DIFFRACTIONt_planar_d0.0042
X-RAY DIFFRACTIONt_plane_restr0.0114

+
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