[English] 日本語
Yorodumi
- PDB-4qr2: Crystal structure of Streptococcus pyogenes Cas2 at pH 7.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qr2
TitleCrystal structure of Streptococcus pyogenes Cas2 at pH 7.5
ComponentsCRISPR-associated endoribonuclease Cas2
KeywordsHYDROLASE / FERREDOXIN-LIKE FOLD / deoxyribonuclease
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / RNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / metal ion binding
Similarity search - Function
CRISPR-associated endonuclease Cas2 / Virulence-associated protein D / CRISPR associated protein Cas2 / CRISPR associated protein Cas2 / Alpha-Beta Plaits - #240 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CRISPR-associated endoribonuclease Cas2
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBae, E. / Ka, D. / Kim, D.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Structural and functional characterization of Streptococcus pyogenes Cas2 protein under different pH conditions
Authors: Ka, D. / Kim, D. / Baek, G. / Bae, E.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CRISPR-associated endoribonuclease Cas2
B: CRISPR-associated endoribonuclease Cas2


Theoretical massNumber of molelcules
Total (without water)22,5242
Polymers22,5242
Non-polymers00
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-11 kcal/mol
Surface area9250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.260, 55.260, 117.821
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein CRISPR-associated endoribonuclease Cas2


Mass: 11261.931 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Gene: cas2, M5005_Spy1285, SPy_1561 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99YS8, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% (w/v) PEG 3350, 200mM MgCl2, 100mM HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 20, 2014
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50.03 Å / Num. obs: 17673 / % possible obs: 99.8 % / Redundancy: 13.7 % / Net I/σ(I): 35.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 14 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 4.63 / Num. unique all: 1723 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ES2

4es2


Resolution: 1.8→50.03 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.895 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23365 888 5.1 %RANDOM
Rwork0.18343 ---
obs0.18581 17516 99.2 %-
all-17658 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.912 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å2-0 Å2
2--0.27 Å2-0 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 0 148 1502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191376
X-RAY DIFFRACTIONr_bond_other_d0.0010.021357
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.9491857
X-RAY DIFFRACTIONr_angle_other_deg0.8833099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0375163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70322.64768
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20115258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0831516
X-RAY DIFFRACTIONr_chiral_restr0.1210.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021523
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0512.258658
X-RAY DIFFRACTIONr_mcbond_other2.0432.256657
X-RAY DIFFRACTIONr_mcangle_it2.6123.376819
X-RAY DIFFRACTIONr_mcangle_other2.6113.378820
X-RAY DIFFRACTIONr_scbond_it3.5632.756718
X-RAY DIFFRACTIONr_scbond_other3.562.757719
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3413.9511039
X-RAY DIFFRACTIONr_long_range_B_refined7.19920.1791638
X-RAY DIFFRACTIONr_long_range_B_other7.07919.3261562
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 64 -
Rwork0.221 1188 -
obs--97.89 %
Refinement TLS params.Method: refined / Origin x: 3.9715 Å / Origin y: 13.6304 Å / Origin z: 24.8299 Å
111213212223313233
T0.0301 Å2-0.0209 Å20.0065 Å2-0.0378 Å2-0.0045 Å2--0.0144 Å2
L1.022 °20.6898 °2-0.8743 °2-2.3557 °2-0.8276 °2--1.6502 °2
S0.1636 Å °-0.0959 Å °0.0547 Å °0.1896 Å °-0.1768 Å °0.0142 Å °-0.1417 Å °0.1107 Å °0.0133 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 83
2X-RAY DIFFRACTION1B1 - 82

+
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