[English] 日本語
Yorodumi
- PDB-4h79: Crystal structure of CasB from Thermobifida fusca -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4h79
TitleCrystal structure of CasB from Thermobifida fusca
ComponentsCRISPR-associated protein, Cse2 family
KeywordsDNA BINDING PROTEIN / CRISPR / Cascade / CasB / CRISPR-assoicated protein / Nucleic acid binding protein
Function / homologyCRISPR-associated protein Cse2 / CRISPR-associated protein Cse2 / Cse2 superfamily / CRISPR-associated protein Cse2 (CRISPR_cse2) / Peroxidase; domain 1 / Orthogonal Bundle / Mainly Alpha / CRISPR-associated protein, Cse2 family
Function and homology information
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKe, A. / Nam, K.H.
CitationJournal: Febs Lett. / Year: 2012
Title: Nucleic acid binding surface and dimer interface revealed by CRISPR-associated CasB protein structures.
Authors: Nam, K.H. / Huang, Q. / Ke, A.
History
DepositionSep 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CRISPR-associated protein, Cse2 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8073
Polymers24,6831
Non-polymers1242
Water1,60389
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.749, 86.749, 70.016
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein CRISPR-associated protein, Cse2 family


Mass: 24682.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Gene: Tfu_1599 / Plasmid: modified pSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star / References: UniProt: Q47PI5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.08 Å3/Da / Density % sol: 60.08 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, pH 8.0-8.5, 2% (v/v) ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 18, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 22861 / % possible obs: 96.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.9→1.93 Å / % possible all: 78.1

-
Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZCA

2zca


Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.507 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1962 1171 5.1 %RANDOM
Rwork0.1476 ---
all0.15 ---
obs0.15 22848 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.48 Å2 / Biso mean: 37.0509 Å2 / Biso min: 14.82 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å21.01 Å20 Å2
2--2.03 Å20 Å2
3----3.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 8 89 1538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191476
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.9521988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2535175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08321.28278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6715255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9891524
X-RAY DIFFRACTIONr_chiral_restr0.1190.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211137
X-RAY DIFFRACTIONr_rigid_bond_restr10.77631476
X-RAY DIFFRACTIONr_sphericity_free28.111525
X-RAY DIFFRACTIONr_sphericity_bonded29.76551517
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 68 -
Rwork0.198 1331 -
all-1399 -
obs--80.26 %
Refinement TLS params.Method: refined / Origin x: -29.2936 Å / Origin y: 32.5466 Å / Origin z: 9.8554 Å
111213212223313233
T0.0189 Å2-0.0079 Å20.0011 Å2-0.0194 Å2-0.0031 Å2--0.0074 Å2
L0.209 °20.0195 °20.2033 °2-0.032 °2-0.1884 °2--1.6712 °2
S0.0174 Å °-0.0221 Å °0.0173 Å °0.0072 Å °-0.0245 Å °0.003 Å °-0.0503 Å °0.1364 Å °0.007 Å °

+
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