[English] 日本語
Yorodumi
- PDB-3i2z: Structure of cold shock protein E from Salmonella typhimurium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3i2z
TitleStructure of cold shock protein E from Salmonella typhimurium
ComponentsRNA chaperone, negative regulator of cspA transcription
KeywordsGENE REGULATION / BETA BARREL / DNA BINDING PROTEIN/TRANSCRIPTION / Cytoplasm
Function / homology
Function and homology information


regulation of gene expression / nucleic acid binding / cytosol
Similarity search - Function
Cold shock, CspA / : / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins ...Cold shock, CspA / : / Cold-shock (CSD) domain / Cold-shock (CSD) domain signature. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RNA chaperone, negative regulator of cspA transcription
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsMorgan, H.P. / McNae, I. / Wear, M.A. / Gallagher, M. / Walkinshaw, M.D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and X-ray structure of cold-shock protein E from Salmonella typhimurium
Authors: Morgan, H.P. / Wear, M.A. / McNae, I. / Gallagher, M.P. / Walkinshaw, M.D.
History
DepositionJun 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: RNA chaperone, negative regulator of cspA transcription
A: RNA chaperone, negative regulator of cspA transcription


Theoretical massNumber of molelcules
Total (without water)15,3712
Polymers15,3712
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA chaperone, negative regulator of cspA transcription


Theoretical massNumber of molelcules
Total (without water)7,6861
Polymers7,6861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: RNA chaperone, negative regulator of cspA transcription


Theoretical massNumber of molelcules
Total (without water)7,6861
Polymers7,6861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.395, 46.798, 46.718
Angle α, β, γ (deg.)90.00, 103.84, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein RNA chaperone, negative regulator of cspA transcription / CSPE / cold shock protein E


Mass: 7685.595 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: 1344 / Description: T7 expression - pET vector was used / Gene: cold shock protein E, cspE / Plasmid: pET28a_CspE / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta BL21(DE3) / References: UniProt: Q7CQZ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 28% PEG 20000, 0.05M AMPSO, 1% glycerol, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.074 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 28, 2006 / Details: Mirrors
RadiationMonochromator: a double crystal Si(III,)with horizontal saggital focusing system
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.074 Å / Relative weight: 1
ReflectionResolution: 1.1→45.36 Å / Num. obs: 47339 / % possible obs: 99.82 % / Observed criterion σ(F): 1.1 / Observed criterion σ(I): 1.1 / Redundancy: 5 % / Rmerge(I) obs: 0.047 / Num. measured all: 260904
Reflection shellResolution: 1.1→1.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.8 / Num. unique all: 7261 / Rsym value: 0.41 / % possible all: 100

-
Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0019refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1MJC; A decapeptide (residues 12-21) from the E. coli cold shock protein A

1mjc


Resolution: 1.1→11.21 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.514 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23424 2532 5.1 %RANDOM
Rwork0.20354 ---
obs0.20506 47339 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.862 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0.92 Å2
2--1.8 Å20 Å2
3----2.51 Å2
Refinement stepCycle: LAST / Resolution: 1.1→11.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1073 0 0 100 1173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221098
X-RAY DIFFRACTIONr_angle_refined_deg1.9351.921479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0585140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87625.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25915185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.446152
X-RAY DIFFRACTIONr_chiral_restr0.3120.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02846
X-RAY DIFFRACTIONr_nbd_refined0.2160.2435
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2786
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3390.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3840.216
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 196 -
Rwork0.349 3476 -
obs--100 %

+
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