[English] 日本語
Yorodumi
- PDB-7lye: Myotoxin I from Bothrops moojeni co-crystallized with synthetic i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lye
TitleMyotoxin I from Bothrops moojeni co-crystallized with synthetic inhibitor Varespladib (LY315920)
ComponentsBasic phospholipase A2 homolog BomoTx
KeywordsTOXIN / Myotoxin I / MjTX-I / PLA2-like
Function / homology
Function and homology information


phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 domain superfamily
Similarity search - Domain/homology
Chem-VRD / Basic phospholipase A2 homolog BomoTx
Similarity search - Component
Biological speciesBothrops moojeni (Brazilian lancehead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.758 Å
AuthorsSalvador, G.H.M. / Borges, R.J. / Fontes, M.R.M.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2021
Title: The synthetic varespladib molecule is a multi-functional inhibitor for PLA 2 and PLA 2 -like ophidic toxins.
Authors: Salvador, G.H.M. / Borges, R.J. / Lomonte, B. / Lewin, M.R. / Fontes, M.R.M.
History
DepositionMar 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Basic phospholipase A2 homolog BomoTx
B: Basic phospholipase A2 homolog BomoTx
C: Basic phospholipase A2 homolog BomoTx
D: Basic phospholipase A2 homolog BomoTx
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2339
Polymers55,3574
Non-polymers1,8765
Water8,053447
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint7 kcal/mol
Surface area24660 Å2
Unit cell
Length a, b, c (Å)60.749, 128.595, 67.790
Angle α, β, γ (deg.)90.000, 106.600, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

21A-423-

HOH

31B-307-

HOH

41B-324-

HOH

51B-362-

HOH

61B-368-

HOH

71C-306-

HOH

-
Components

#1: Protein
Basic phospholipase A2 homolog BomoTx / svPLA2 homolog


Mass: 13839.158 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bothrops moojeni (Brazilian lancehead) / Tissue: Venom Gland / References: UniProt: A0A1S5XW05
#2: Chemical
ChemComp-VRD / ({3-[amino(oxo)acetyl]-1-benzyl-2-ethyl-1H-indol-4-yl}oxy)acetic acid / Varespladib / Varespladib


Mass: 380.394 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H20N2O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antiinflammatory, inhibitor*YM
#3: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.29 Å3/Da / Density % sol: 46.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 32% w/v PEG4000, 0.1 M Tris HCl, 0.1 M lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.425 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 12, 2018 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 1.758→32.483 Å / Num. obs: 328716 / % possible obs: 99.09 % / Redundancy: 6.7 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.025 / Rrim(I) all: 0.064 / Net I/σ(I): 19.98
Reflection shellResolution: 1.758→1.82 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 1.24 / Num. unique obs: 49048 / CC1/2: 0.584 / CC star: 0.859 / Rpim(I) all: 0.604 / Rrim(I) all: 0.159 / % possible all: 97.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.33 Å47.6 Å
Translation6.33 Å47.6 Å

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.8.1phasing
PHENIX1.13-2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CE2

6ce2


Resolution: 1.758→32.483 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 3940 4.08 %
Rwork0.1936 92550 -
obs0.1948 96490 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.4 Å2 / Biso mean: 45.3403 Å2 / Biso min: 20.83 Å2
Refinement stepCycle: final / Resolution: 1.758→32.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3735 0 136 447 4318
Biso mean--40.21 45.7 -
Num. residues----488
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.758-1.7790.3771360.3845322494
1.779-1.80150.37991380.3628324298
1.8015-1.82520.34461400.3373336398
1.8252-1.85020.34271400.3289324598
1.8502-1.87670.31561410.2975335098
1.8767-1.90470.32171400.3083324098
1.9047-1.93440.33981420.2841329198
1.9344-1.96610.31161430.2761333999
1.9661-20.29021390.2667330698
2-2.03640.2691410.2701331999
2.0364-2.07560.32171400.259326998
2.0756-2.11790.30881420.2481330099
2.1179-2.1640.31691440.2405334799
2.164-2.21430.25731370.2216328399
2.2143-2.26960.29241430.2219338099
2.2696-2.3310.23491400.2136332599
2.331-2.39960.21461440.20123313100
2.3996-2.4770.23621370.2013360100
2.477-2.56550.22241430.20383342100
2.5655-2.66820.24751420.2065332799
2.6682-2.78950.22861430.1948334099
2.7895-2.93650.20891410.1965328498
2.9365-3.12030.24291430.1959330899
3.1203-3.3610.19281420.1806333199
3.361-3.69880.23281370.161318195
3.6988-4.23310.16541450.144332299
4.2331-5.32940.16241440.14143345100
5.3294-32.4830.18851330.1617327497
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)
19.0861-1.91021.165.2576-1.86442.17870.19540.1920.4992-0.0095-0.1205-0.60640.04110.21620.04250.272-0.03560.01290.3022-0.05230.3474-0.055617.399865.4688
24.3801-1.5640.31533.7538-0.59764.756-0.0141-0.177-0.55210.01280.06410.17230.1762-0.0082-0.08340.17390.0152-0.03740.2188-0.0080.3746-0.78384.338472.6093
36.37250.3731-1.08282.71930.84597.5079-0.16310.8109-0.9317-1.00930.0875-0.35350.01720.2632-0.06980.52570.062-0.1190.4507-0.19870.5271-7.66995.814756.4701
42.2238-1.3197-0.2983.271-0.13631.28530.02030.0626-0.0644-0.13350.00210.276-0.12070.0316-0.08320.2585-0.0042-0.06990.2633-0.04780.3815-7.965315.058268.1492
54.74976.4006-1.18812.0996-1.30233.3687-0.2429-0.08930.3611-0.57340.08070.0277-0.14950.27480.2160.38010.05350.05180.44660.06190.80526.82720.793275.0584
64.80451.15991.5838.55311.65328.6915-0.17030.5616-0.3304-0.0247-0.06340.11740.5320.47120.20580.2781-0.04420.05420.2998-0.04180.2192-0.999535.612864.6471
72.8784-0.60230.9874.32-2.27272.544-0.02370.30080.10690.4999-0.04270.8835-0.22890.05430.02570.2399-0.05840.1060.2735-0.04990.3834-8.743146.039859.4502
86.5752-0.7671-0.04035.1342-1.09055.85860.5353-0.1270.34520.3716-0.5755-0.1596-0.52890.32030.01860.4922-0.1811-0.0130.4019-0.00150.29735.384947.290469.6643
91.9252-0.9571-0.44555.4521-1.70420.92540.4619-0.22180.0391.2616-0.1842-0.0397-0.36740.5291-0.21780.4725-0.14450.03430.4181-0.00320.2433-0.998733.675375.7322
104.2567-0.09931.5873.6879-0.43513.83740.18750.1089-0.14330.6309-0.06630.7956-0.10730.0249-0.0280.4373-0.06710.18790.2284-0.04410.4298-9.150340.174464.7695
113.8114-5.23551.03757.842-1.76870.4471-0.06330.94210.4079-0.7855-0.19430.44560.03730.0590.20290.5821-0.0254-0.12540.6654-0.19810.5356-11.053146.680546.9431
128.4077-5.86031.04237.5032-0.56823.2525-0.2274-0.5366-0.27261.01950.47660.84970.4315-1.0449-0.24620.4023-0.03490.12090.34560.00450.4887-14.210957.214559.1335
131.10390.3658-0.43575.1058-0.16096.686-0.02740.0919-0.1287-0.03880.0727-0.63340.68510.3179-0.11620.503-0.0814-0.06670.40490.00930.405517.611953.381392.6252
143.6411.37571.0086.81330.057.2587-0.00880.10820.40780.39940.52610.3028-0.5393-0.3096-0.43910.5572-0.0698-0.01750.38030.10160.325511.000264.145392.7604
154.14721.3820.1614.5387-1.00733.64140.2222-0.72890.08430.8076-0.4078-0.337-0.09260.3250.14760.8221-0.1214-0.18140.48760.04530.352117.032653.5761106.1495
164.80012.47651.70443.09253.84395.4725-0.161-0.77890.30620.9196-0.7112-0.38340.17010.27140.26791.0716-0.15-0.21570.45960.06170.312213.536652.9777111.3003
172.39871.04250.0782.99360.25946.02620.0302-0.121-0.09120.15320.2556-0.0970.0412-0.7485-0.22520.6156-0.1213-0.07580.35860.08170.304510.465754.746595.4566
186.1678-0.73882.69585.8238-1.26675.803-0.29572.0454-0.6689-0.6537-1.199-0.4714-0.30320.68081.32220.9028-0.12670.11741.1339-0.06670.574218.147462.787578.5747
199.2019-3.3504-5.35996.44843.53893.5978-0.5630.74670.13310.49920.37940.89790.2335-1.2881-0.12480.7279-0.04980.00840.48250.15720.431410.331372.751388.8707
204.02130.3328-0.75731.9265-0.33511.0387-0.90520.9386-0.4807-0.52170.4495-0.1244-0.44150.1550.31471.0089-0.40980.08840.5725-0.10610.357317.053732.486395.8452
211.7729-1.86191.45762.7063-0.35894.4947-0.14150.139-0.165-0.50370.4463-0.1760.22680.2443-0.35380.5501-0.0992-0.00460.3628-0.08210.299816.111922.04104.8329
222.542-1.02321.17862.0782-0.67830.6408-0.03560.6995-0.5669-1.49530.27050.2347-0.20720.5484-0.29091.31-0.31850.01650.6572-0.03710.382513.143628.226888.2675
231.8707-0.9043-0.60892.40341.46964.4268-0.01440.2172-0.0927-0.61470.284-0.0799-0.1696-0.1847-0.14940.7499-0.1667-0.05450.34990.0090.259111.340627.5043101.3295
241.40831.9452-1.83847.97110.04884.0616-0.0626-0.84830.07680.0741-0.0545-0.9786-0.02030.02990.07460.58140.0614-0.2020.4827-0.12740.526519.774816.636111.9051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 21 )A1 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 53 )A22 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 65 )A54 - 65
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 107 )A66 - 107
5X-RAY DIFFRACTION5chain 'A' and (resid 108 through 122 )A108 - 122
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 13 )B1 - 13
7X-RAY DIFFRACTION7chain 'B' and (resid 14 through 53 )B14 - 53
8X-RAY DIFFRACTION8chain 'B' and (resid 54 through 65 )B54 - 65
9X-RAY DIFFRACTION9chain 'B' and (resid 66 through 79 )B66 - 79
10X-RAY DIFFRACTION10chain 'B' and (resid 80 through 107 )B80 - 107
11X-RAY DIFFRACTION11chain 'B' and (resid 108 through 115 )B108 - 115
12X-RAY DIFFRACTION12chain 'B' and (resid 116 through 122 )B116 - 122
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 31 )C1 - 31
14X-RAY DIFFRACTION14chain 'C' and (resid 32 through 53 )C32 - 53
15X-RAY DIFFRACTION15chain 'C' and (resid 54 through 72 )C54 - 72
16X-RAY DIFFRACTION16chain 'C' and (resid 73 through 79 )C73 - 79
17X-RAY DIFFRACTION17chain 'C' and (resid 80 through 107 )C80 - 107
18X-RAY DIFFRACTION18chain 'C' and (resid 108 through 115 )C108 - 115
19X-RAY DIFFRACTION19chain 'C' and (resid 116 through 122 )C116 - 122
20X-RAY DIFFRACTION20chain 'D' and (resid 1 through 13 )D1 - 13
21X-RAY DIFFRACTION21chain 'D' and (resid 14 through 53 )D14 - 53
22X-RAY DIFFRACTION22chain 'D' and (resid 54 through 79 )D54 - 79
23X-RAY DIFFRACTION23chain 'D' and (resid 80 through 107 )D80 - 107
24X-RAY DIFFRACTION24chain 'D' and (resid 108 through 122 )D108 - 122

+
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