[English] 日本語
Yorodumi
- PDB-5yjd: Structural insights into the CRISPR-Cas-associated ribonuclease a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yjd
TitleStructural insights into the CRISPR-Cas-associated ribonuclease activity of Staphylococcus epidermidis Csm3
ComponentsCsm3
KeywordsHYDROLASE / CRISPR-Associated Proteins / ferredoxin-like fold / Staphylococcus epidermidis
Function / homology
Function and homology information


endonuclease activity / defense response to virus / hydrolase activity / RNA binding / metal ion binding
Similarity search - Function
CRISPR-associated RAMP Csm3 / : / CRISPR type III-associated protein / RAMP superfamily
Similarity search - Domain/homology
CRISPR system Cms endoribonuclease Csm3
Similarity search - Component
Biological speciesStaphylococcus epidermidis RP62A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsZhao, Y.Q. / Gu, Y.J. / Zhu, X.F. / Cheng, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570842 China
CitationJournal: To Be Published
Title: Structural insights into the CRISPR-Cas-associated ribonuclease activity of Staphylococcus epidermidis Csm3 and Csm6
Authors: Zhao, Y.Q. / Gu, Y.J. / Zhu, X.F. / Cheng, W.
History
DepositionOct 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Csm3
B: Csm3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5353
Polymers50,4952
Non-polymers401
Water1,22568
1
A: Csm3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2872
Polymers25,2471
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-8 kcal/mol
Surface area10580 Å2
MethodPISA
2
B: Csm3


Theoretical massNumber of molelcules
Total (without water)25,2471
Polymers25,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.623, 105.760, 155.977
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 3 - 216 / Label seq-ID: 3 - 216

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Csm3 / Csm3


Mass: 25247.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis RP62A (bacteria)
Strain: ATCC 35984 / RP62A / Gene: SERP2459 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HK91
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.16M Calcium acetate, 14% (w/v) PEG8000, 20% (w/v) glycerol, 0.08M Sodium cacodylate pH6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.26→52.88 Å / Num. obs: 21671 / % possible obs: 98.54 % / Redundancy: 12.2 % / Net I/σ(I): 18.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→52.88 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 17.767 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.209 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24097 1143 5 %RANDOM
Rwork0.19697 ---
obs0.19917 21671 98.53 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 68.99 Å2
Baniso -1Baniso -2Baniso -3
1-3.46 Å20 Å20 Å2
2--2.72 Å20 Å2
3----6.18 Å2
Refinement stepCycle: 1 / Resolution: 2.26→52.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2925 0 1 68 2994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193018
X-RAY DIFFRACTIONr_bond_other_d0.0020.022817
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9534052
X-RAY DIFFRACTIONr_angle_other_deg0.9436539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3885370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24224.403159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92915561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9461525
X-RAY DIFFRACTIONr_chiral_restr0.0910.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023377
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02624
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_it2.882.6961489
X-RAY DIFFRACTIONr_mcbond_other2.8752.6921488
X-RAY DIFFRACTIONr_mcangle_it4.5474.0151856
X-RAY DIFFRACTIONr_mcangle_other4.5464.0211857
X-RAY DIFFRACTIONr_scbond_it4.2253.1321529
X-RAY DIFFRACTIONr_scbond_other4.2253.1351530
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6044.5342197
X-RAY DIFFRACTIONr_long_range_B_refined8.84930.9663137
X-RAY DIFFRACTIONr_long_range_B_other8.85530.9093132
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11216 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.26→2.319 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 70 -
Rwork0.373 1375 -
obs--86.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5262-0.33390.43332.5031-1.49158.64210.04420.288-0.0038-0.3113-0.09160.05440.38690.1440.04740.18240.04360.03080.16310.02180.4056-8.7347-14.9221-20.5473
25.0986-1.52441.55822.5164-1.89984.07750.27660.2971-0.0484-0.3073-0.3325-0.47160.30050.68260.05590.19320.01860.06990.27910.03610.4763.067-18.098-15.445
32.0736-0.4551.25121.8701-1.48755.33410.00410.26120.0988-0.35640.04450.0374-0.0153-0.1308-0.04860.21950.01240.01140.16180.02410.3764-11.687-12.7583-24.1331
43.1709-0.47922.06493.2237-2.00218.2504-0.07840.3050.47480.0369-0.1317-0.4213-0.63920.87540.21010.2028-0.07440.01520.20230.04120.5296-0.4964-7.7191-15.1647
56.6395-2.14961.44856.0445-2.27458.149-0.2958-0.61880.55560.60620.2295-0.2783-0.9584-0.01920.06630.31540.0590.00990.2558-0.09370.3427-8.0078-10.21860.8531
62.0357-0.3414-1.12833.0810.20237.2402-0.16420.17380.04130.69130.2622-0.2463-0.596-0.0004-0.0980.71190.0990.04790.18320.07850.4515-20.982816.0077-23.7337
71.4314-2.0975-0.96474.64431.34892.8392-0.4497-0.0783-0.05771.04440.19080.3459-0.0791-0.23850.25890.83490.07520.10820.22170.07110.3376-26.663615.1603-18.884
83.7877-1.3875-3.07843.53662.38653.0270.15970.4620.00940.0472-0.25990.2052-0.0838-0.42360.10020.4023-0.03490.05170.27640.07380.3529-21.12210.9699-39.246
94.17380.1184-0.45474.06951.70625.9685-0.4160.0364-0.38371.25840.08590.54320.219-0.51150.33010.95360.10810.26560.16780.1080.3993-29.631410.2921-15.6543
109.67253.25924.85038.32964.42546.1269-0.347-0.7638-0.76782.54380.0822-0.18381.2858-0.01270.26481.70370.25340.15060.50150.22590.4748-24.80979.4567-1.022
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 38
2X-RAY DIFFRACTION2A39 - 92
3X-RAY DIFFRACTION3A93 - 157
4X-RAY DIFFRACTION4A158 - 197
5X-RAY DIFFRACTION5A198 - 214
6X-RAY DIFFRACTION6B3 - 42
7X-RAY DIFFRACTION7B43 - 114
8X-RAY DIFFRACTION8B115 - 147
9X-RAY DIFFRACTION9B148 - 200
10X-RAY DIFFRACTION10B201 - 214

+
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