[English] 日本語
Yorodumi
- PDB-6szz: Crystal structure of Cold Shock Protein B (CspB) containing the m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6szz
TitleCrystal structure of Cold Shock Protein B (CspB) containing the modified residue 4-F-Trp
ComponentsCold shock protein CspD
KeywordsSTRUCTURAL PROTEIN / fluorine cold shock domain
Function / homology
Function and homology information


regulation of RNA metabolic process / nucleoid / regulation of gene expression / nucleic acid binding / DNA binding / cytoplasm
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
Cold shock protein CspD / Cold shock protein CspB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsZhou, T. / Mayans, O.
CitationJournal: Sci Rep / Year: 2020
Title: What does fluorine do to a protein? Thermodynamic, and highly-resolved structural insights into fluorine-labelled variants of the cold shock protein.
Authors: Welte, H. / Zhou, T. / Mihajlenko, X. / Mayans, O. / Kovermann, M.
History
DepositionOct 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cold shock protein CspD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5743
Polymers7,3901
Non-polymers1842
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint0 kcal/mol
Surface area4650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.050, 56.050, 55.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

#1: Protein Cold shock protein CspD / Cold-shock protein / Cold-shock protein CspB / Major cold shock protein / Putative cold-shock DNA- ...Cold-shock protein / Cold-shock protein CspB / Major cold shock protein / Putative cold-shock DNA-binding protein


Mass: 7390.118 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria)
Gene: B4122_0412, B4417_4327, CJ481_22435, DFO69_3150, ETA10_05025, ETK61_05130, ETL41_18150, FA024_03420, SC09_Contig19orf00064
Production host: Escherichia coli (E. coli) / References: UniProt: A0A063XII3, UniProt: P32081*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS propane pH 7.0,1.2 M Sodium citrate tribasic dihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→39.64 Å / Num. obs: 5913 / % possible obs: 99.8 % / Redundancy: 24.75 % / Biso Wilson estimate: 50.99 Å2 / CC1/2: 1 / Rsym value: 0.075 / Net I/σ(I): 28.89
Reflection shellResolution: 2.05→2.15 Å / Num. unique obs: 762 / CC1/2: 0.584 / Rsym value: 2.735

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CSP

1csp


Resolution: 2.05→39.64 Å / SU ML: 0.2461 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.9561
RfactorNum. reflection% reflection
Rfree0.2312 306 5.2 %
Rwork0.2083 --
obs0.2097 5879 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms518 0 12 18 548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077538
X-RAY DIFFRACTIONf_angle_d0.9216719
X-RAY DIFFRACTIONf_chiral_restr0.049672
X-RAY DIFFRACTIONf_plane_restr0.004896
X-RAY DIFFRACTIONf_dihedral_angle_d13.5021306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.580.30361310.27752723X-RAY DIFFRACTION99.62
2.58-39.640.22271750.19622850X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.596043507 Å / Origin y: 7.78346539785 Å / Origin z: 11.6198798494 Å
111213212223313233
T0.377010031814 Å2-0.0315933112551 Å20.109619798831 Å2-0.38150403697 Å20.0532726482054 Å2--0.425244209097 Å2
L9.54906048378 °20.0100476034183 °21.96694878811 °2-8.73119497738 °21.99931257807 °2--8.94174857216 °2
S-0.133252229447 Å °-1.07173111564 Å °-0.450624267587 Å °0.701741666802 Å °-0.0672138493476 Å °0.236325813589 Å °0.572346831448 Å °-0.380191896832 Å °0.14803660164 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 67)

+
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