[English] 日本語
Yorodumi
- PDB-6ls1: Ribonuclease from Hericium erinaceus active and GMP binding form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ls1
TitleRibonuclease from Hericium erinaceus active and GMP binding form
ComponentsRibonuclease T1
KeywordsRNA BINDING PROTEIN / RNA Binding Endoribonuclease Activity Ribonuclease Activity
Function / homology: / ribonuclease / Ribonuclease/ribotoxin / RNA endonuclease activity / RNA binding / GUANOSINE / DI(HYDROXYETHYL)ETHER / Ribonuclease T1
Function and homology information
Biological speciesHericium erinaceus (bearded tooth)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsTakebe, K. / Suzuki, M. / Sangawa, T. / Kobayashi, H. / Itagaki, T.
CitationJournal: To Be Published
Title: Ribonuclease from Hericium erinaceus active and GMP binding form
Authors: Takebe, K. / Suzuki, M. / Sangawa, T. / Kobayashi, H.
History
DepositionJan 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Ribonuclease T1
B: Ribonuclease T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9165
Polymers21,4312
Non-polymers4853
Water3,675204
1
A: Ribonuclease T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1053
Polymers10,7151
Non-polymers3892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5260 Å2
MethodPISA
2
B: Ribonuclease T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8112
Polymers10,7151
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-16 kcal/mol
Surface area5260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.760, 97.760, 68.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 4 or resid 7...
21(chain B and (resid 2 through 4 or resid 7...

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
11SERSERGLYGLY(chain A and (resid 2 through 4 or resid 7...AA2 - 42 - 4
12CYSCYSARGARG(chain A and (resid 2 through 4 or resid 7...AA7 - 107 - 10
13TYRTYRSERSER(chain A and (resid 2 through 4 or resid 7...AA12 - 1312 - 13
14GLNGLNPHEPHE(chain A and (resid 2 through 4 or resid 7...AA1 - 1001 - 100
15GLYGLYCYSCYS(chain A and (resid 2 through 4 or resid 7...AA94 - 9894 - 98
16GLYGLYCYSCYS(chain A and (resid 2 through 4 or resid 7...AA94 - 9894 - 98
17PHEPHEPHEPHE(chain A and (resid 2 through 4 or resid 7...AA100100
21SERSERGLYGLY(chain B and (resid 2 through 4 or resid 7...BB2 - 42 - 4
22CYSCYSARGARG(chain B and (resid 2 through 4 or resid 7...BB7 - 107 - 10
23TYRTYRSERSER(chain B and (resid 2 through 4 or resid 7...BB12 - 1312 - 13
24SERSERGLYGLY(chain B and (resid 2 through 4 or resid 7...BB15 - 2615 - 26
25GLNGLNPHEPHE(chain B and (resid 2 through 4 or resid 7...BB1 - 1001 - 100
26GLYGLYCYSCYS(chain B and (resid 2 through 4 or resid 7...BB94 - 9894 - 98
27GLYGLYCYSCYS(chain B and (resid 2 through 4 or resid 7...BB94 - 9894 - 98
28PHEPHEPHEPHE(chain B and (resid 2 through 4 or resid 7...BB100100

-
Components

#1: Protein Ribonuclease T1 /


Mass: 10715.292 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hericium erinaceus (bearded tooth) / Gene: RNHe1 / Production host: Escherichia coli (E. coli) / References: UniProt: B1Q4V2
#2: Chemical ChemComp-GMP / GUANOSINE / Guanosine


Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 1.92 Å3/Da / Density % sol: 35.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.4M Magnesium sulfate, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.58→48.88 Å / Num. obs: 23162 / % possible obs: 100 % / Redundancy: 22.6 % / CC1/2: 0.999 / Net I/σ(I): 23.3
Reflection shellResolution: 1.58→1.61 Å / Num. unique obs: 23162 / CC1/2: 0.999

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GY6

5gy6


Resolution: 1.58→8.793 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1902 1129 4.91 %
Rwork0.1489 21864 -
obs0.1509 22993 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.08 Å2 / Biso mean: 21.3684 Å2 / Biso min: 7.37 Å2
Refinement stepCycle: final / Resolution: 1.58→8.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 32 207 1738
Biso mean--19.62 33.05 -
Num. residues----200
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A506X-RAY DIFFRACTION6.079TORSIONAL
12B506X-RAY DIFFRACTION6.079TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.58-1.65150.22851430.166226772820
1.6515-1.73790.20781350.158326932828
1.7379-1.84590.20061370.155127122849
1.8459-1.98690.22141370.153727042841
1.9869-2.1840.19371440.148927152859
2.184-2.49370.18341470.150627382885
2.4937-3.11840.19061450.152827512896
3.1184-8.79280.17251410.139528743015
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)
11.8366-0.53920.99343.1262-0.43571.7029-0.01610.0206-0.00580.05150.130.00550.05120.0312-0.10170.0606-0.00780.00530.0873-0.01460.085717.0035-8.1819-17.0519
22.3058-0.7488-0.15422.928-0.01072.9093-0.2419-0.2189-0.13760.47870.1535-0.0706-0.04730.10480.05080.22980.03810.0020.09520.00450.083234.7806-13.82872.851
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 100)A1 - 100
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 100)B1 - 100

+
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