[English] 日本語
Yorodumi
- PDB-7ty1: Crystal structure of apo eosinophil cationic protein (ribonucleas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ty1
TitleCrystal structure of apo eosinophil cationic protein (ribonuclease 3) from Macaca fascicularis (MfECP)
ComponentsEosinophil cationic protein
KeywordsHYDROLASE / MfECP / RNase 3 / ribonuclease / crab-eating macaque / long-tailed macaque / cynomolgus monkey / eosinophil cationic protein / ECP.
Function / homology
Function and homology information


RNA metabolic process / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / endonuclease activity / nucleic acid binding / extracellular region
Similarity search - Function
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / Eosinophil cationic protein
Similarity search - Component
Biological speciesMacaca fascicularis (crab-eating macaque)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsTran, T.T.Q. / Pham, N.T.H. / Calmettes, C. / Doucet, N.
Funding support United States, Canada, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM105978 United States
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN201605557 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN201706091 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)CREATE511956 Canada
Fonds de Recherche du Quebec - Sante (FRQS)251848 Canada
Fonds de Recherche du Quebec - Sante (FRQS)281993 Canada
CitationJournal: To Be Published
Title: Crystal structure of apo eosinophil cationic protein (ribonuclease 3) from Macaca fascicularis (MfECP)
Authors: Thi Thanh, Q.T. / Pham, N.T.H. / Calmettes, C. / Doucet, N.
History
DepositionFeb 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Eosinophil cationic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9718
Polymers15,9121
Non-polymers1,0597
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.330, 39.270, 76.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Eosinophil cationic protein / / ECP / Ribonuclease 3 / RNase 3


Mass: 15912.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca fascicularis (crab-eating macaque)
Gene: RNASE3, RNS3 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P47779, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.75 Å3/Da / Density % sol: 29.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1M Citric acid pH 3.5, 25% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.23985 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 1.8→38.02 Å / Num. obs: 10862 / % possible obs: 100 % / Redundancy: 12 % / CC1/2: 0.998 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.049 / Rrim(I) all: 0.169 / Net I/σ(I): 14.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.8-1.8612.80.783.610760.90.2270.814100
1.86-1.9412.30.6384.810410.9490.1880.666100
1.94-2.0312.60.536.710610.9740.1540.553100
2.03-2.1312.60.4069.210560.9870.1180.432100
2.13-2.2712.40.35910.910920.9880.1060.375100
2.27-2.4412.10.28113.210660.9920.0830.294100
2.44-2.6912.20.22116.310870.9920.0660.231100
2.69-3.0811.70.16220.310890.9950.0490.17100
3.08-3.88110.10225.511160.9970.0320.107100
3.88-38.0210.30.0729.14780.9980.0220.073100

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å38.01 Å

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QMT

1qmt


Resolution: 1.8→38.01 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 23.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2498 1084 9.98 %
Rwork0.2067 9776 -
obs0.2109 10860 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.67 Å2 / Biso mean: 28.9247 Å2 / Biso min: 6.5 Å2
Refinement stepCycle: final / Resolution: 1.8→38.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1113 0 117 78 1308
Biso mean--46.26 31.79 -
Num. residues----134
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
1.8-1.880.33681290.269911961325
1.88-1.980.27011350.219311951330
1.98-2.110.23431350.203211911326
2.11-2.270.26891300.206812141344
2.27-2.50.2641430.197811971340
2.5-2.860.27441280.208212261354
2.86-3.60.27061370.190612431380
3.6-38.010.20461470.208313141461
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)
10.01980.016-0.00660.02560.01250.01260.02080.1276-0.0242-0.0395-0.07060.0407-0.0666-0.0802-0.01940.04840.00750.01180.09-0.00890.059217.77423.5773-9.4006
20.04160.0382-0.00080.03560.01830.02690.11770.0083-0.0410.1041-0.07850.0047-0.25060.04190.00070.182-0.00320.00410.09870.01470.118419.00834.0245-21.5113
30.0812-0.0081-0.10710.06870.01060.0949-0.05950.1720.0127-0.0694-0.12250.13350.0331-0.202-0.04060.08170.03490.00640.165-0.03830.13377.83063.097-13.2835
40.01340.01810.03440.03730.05730.10960.03540.0537-0.06070.05030.076-0.04360.03780.04480.12870.2878-0.08770.18420.0176-0.21260.30193.8694-8.36-3.8889
50.00330.0003-0.00760.004-0.00210.00380.02890.0029-0.0061-0.0325-0.09320.05460.058-0.04280.00270.13520.04880.00010.2005-0.0590.1362-1.83612.7184-14.6524
60.01590.0148-0.00270.4907-0.12540.04270.04690.04340.0325-0.1204-0.0863-0.14570.0029-0.0354-0.04530.0908-0.00160.01350.1038-0.00140.05816.0372-1.8535-27.52
70.0402-0.04720.01710.3852-0.060.0284-0.11090.2149-0.12220.11120.04060.07690.1185-0.0578-0.11260.0912-0.03840.03120.1384-0.04660.12738.4681.9-4.694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 0:17)A0 - 17
2X-RAY DIFFRACTION2(chain A and resid 18:36)A18 - 36
3X-RAY DIFFRACTION3(chain A and resid 37:55)A37 - 55
4X-RAY DIFFRACTION4(chain A and resid 56:73)A56 - 73
5X-RAY DIFFRACTION5(chain A and resid 74:81)A74 - 81
6X-RAY DIFFRACTION6(chain A and resid 82:104)A82 - 104
7X-RAY DIFFRACTION7(chain A and resid 105:133)A105 - 133

+
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