[English] 日本語
Yorodumi
- PDB-7xz3: Crystal structure of the Type I-B CRISPR-associated protein, Csh2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7xz3
TitleCrystal structure of the Type I-B CRISPR-associated protein, Csh2 from Thermobaculum terrenum
ComponentsCRISPR-associated protein, Csh2 family
KeywordsTRANSFERASE / RNA BINDING PROTEIN
Function / homologyCRISPR-associated protein Csh2 / CRISPR-associated protein Cas7, subtype I-B/I-C / CRISPR-associated protein Cas7 / maintenance of CRISPR repeat elements / CRISPR-associated protein, Csh2 family
Function and homology information
Biological speciesThermobaculum terrenum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.889 Å
AuthorsSeo, P.W. / Gu, D.H. / Park, S.Y. / Kim, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Biochim Biophys Acta Proteins Proteom / Year: 2023
Title: Structural characterization of the type I-B CRISPR Cas7 from Thermobaculum terrenum.
Authors: Seo, P.W. / Gu, D.H. / Kim, J.W. / Kim, J.H. / Park, S.Y. / Kim, J.S.
History
DepositionJun 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CRISPR-associated protein, Csh2 family
B: CRISPR-associated protein, Csh2 family


Theoretical massNumber of molelcules
Total (without water)73,3802
Polymers73,3802
Non-polymers00
Water7,278404
1
A: CRISPR-associated protein, Csh2 family


Theoretical massNumber of molelcules
Total (without water)36,6901
Polymers36,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CRISPR-associated protein, Csh2 family


Theoretical massNumber of molelcules
Total (without water)36,6901
Polymers36,6901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.946, 54.432, 96.364
Angle α, β, γ (deg.)106.500, 91.490, 90.090
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 15 or resid 30...
21(chain B and (resid 1 through 15 or resid 30 through 63 or resid 68 through 319))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYS(chain A and (resid 1 through 15 or resid 30...AA1 - 157 - 21
12ARGARGARGARG(chain A and (resid 1 through 15 or resid 30...AA30 - 6336 - 69
13GLYGLYASNASN(chain A and (resid 1 through 15 or resid 30...AA68 - 14874 - 154
14ARGARGLYSLYS(chain A and (resid 1 through 15 or resid 30...AA176 - 223182 - 229
15GLYGLYSERSER(chain A and (resid 1 through 15 or resid 30...AA225 - 319231 - 325
21METMETLYSLYS(chain B and (resid 1 through 15 or resid 30 through 63 or resid 68 through 319))BB1 - 157 - 21
22ARGARGARGARG(chain B and (resid 1 through 15 or resid 30 through 63 or resid 68 through 319))BB30 - 6336 - 69
23GLYGLYSERSER(chain B and (resid 1 through 15 or resid 30 through 63 or resid 68 through 319))BB68 - 31974 - 325

-
Components

#1: Protein CRISPR-associated protein, Csh2 family


Mass: 36690.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobaculum terrenum (bacteria) / Gene: Tter_2426 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D1CHV0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.13 Å3/Da / Density % sol: 42.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 7 % (w/v) Polyethylene glycol 3350, 2 % (v/v) Tacsimate pH 5.0, 0.1 M Sodium citrate pH 5.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.889→20 Å / Num. obs: 46406 / % possible obs: 96.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.042 / Rrim(I) all: 0.079 / Χ2: 0.755 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.933.20.55723200.7820.3620.6670.47695.4
1.93-1.973.30.49822840.8360.3190.5940.48695
1.97-2.013.30.45122230.8470.2910.5390.48895.4
2.01-2.053.20.33923050.9050.2230.4080.51995.4
2.05-2.093.20.30623040.9190.2010.3680.54495.1
2.09-2.143.50.2822660.930.1730.3310.52896.3
2.14-2.193.50.23423430.940.1440.2750.59995.9
2.19-2.253.50.20823020.9620.1270.2440.6396
2.25-2.323.50.18122770.9650.1120.2130.64996.2
2.32-2.393.40.15523510.9690.0980.1840.67396.4
2.39-2.483.30.13123040.9740.0840.1560.69596.8
2.48-2.583.30.11523320.9810.0740.1370.72396.7
2.58-2.693.60.10223280.9860.0620.1190.78197.6
2.69-2.843.60.08923770.9870.0550.1050.88397.2
2.84-3.013.60.07422910.9910.0460.0870.9397.8
3.01-3.253.40.06623520.9920.0420.0791.00698.2
3.25-3.573.60.0623660.9930.0370.071.08798.3
3.57-4.083.70.05123490.9950.0310.061.06998.6
4.08-5.133.40.04324050.9960.0280.0511.09698.2
5.13-203.60.03923270.9980.0240.0451.01898.2

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7KHA

7kha


Resolution: 1.889→19.895 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 22.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2208 1851 3.99 %
Rwork0.177 44542 -
obs0.1788 46393 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.95 Å2 / Biso mean: 38.7092 Å2 / Biso min: 17.74 Å2
Refinement stepCycle: final / Resolution: 1.889→19.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4374 0 0 404 4778
Biso mean---49.58 -
Num. residues----543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034444
X-RAY DIFFRACTIONf_angle_d0.6885997
X-RAY DIFFRACTIONf_chiral_restr0.047673
X-RAY DIFFRACTIONf_plane_restr0.003768
X-RAY DIFFRACTIONf_dihedral_angle_d11.4662681
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2590X-RAY DIFFRACTION7.424TORSIONAL
12B2590X-RAY DIFFRACTION7.424TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.889-1.940.27941310.2368315087
1.94-1.99710.25541270.2269334795
1.9971-2.06150.2471510.2053341695
2.0615-2.1350.24311300.1969338396
2.135-2.22040.23051590.1873345296
2.2204-2.32130.26031310.1935342796
2.3213-2.44350.27031420.1904340996
2.4435-2.59630.22821460.1874350197
2.5963-2.79630.28631480.1895344797
2.7963-3.07670.24431480.1941349598
3.0767-3.51980.211500.1758350398
3.5198-4.42650.17561410.1496353599
4.4265-19.8950.20151470.1615347798
Refinement TLS params.Method: refined / Origin x: 24.2503 Å / Origin y: 63.1419 Å / Origin z: 26.0495 Å
111213212223313233
T0.1912 Å20.002 Å20.0023 Å2-0.2101 Å2-0.0292 Å2--0.2061 Å2
L0.2459 °20.008 °20.0642 °2-0.4352 °2-0.3502 °2--0.4076 °2
S0.0283 Å °-0.0049 Å °-0.014 Å °-0.0591 Å °-0.015 Å °0.014 Å °0.0705 Å °0.011 Å °-0.0083 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 319
2X-RAY DIFFRACTION1allB1 - 319
3X-RAY DIFFRACTION1allS1 - 409

+
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