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- PDB-7ty1: Crystal structure of apo eosinophil cationic protein (ribonucleas... -

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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


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: J.Biol.Chem. / Year: 2024
Title: Ancestral sequence reconstruction dissects structural and functional differences among eosinophil ribonucleases.
Authors: Tran, T.T.Q. / Narayanan, C. / Loes, A.N. / Click, T.H. / Pham, N.T.H. / Letourneau, M. / Harms, M.J. / Calmettes, C. / Agarwal, P.K. / Doucet, N.
History
DepositionFeb 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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


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


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


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

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Experimental details

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Experiment

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

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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

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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

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Phasing

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

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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

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