[English] 日本語
Yorodumi
- PDB-4yu7: Crystal structure of Piratoxin I (PrTX-I) complexed to caffeic acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yu7
TitleCrystal structure of Piratoxin I (PrTX-I) complexed to caffeic acid
ComponentsBasic phospholipase A2 homolog piratoxin-1
KeywordsTOXIN / Phospholipase A2 Phospholipase A2-like Bothrops snake venom inhibitor
Function / homology
Function and homology information


A2-type glycerophospholipase activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CAFFEIC ACID / Basic phospholipase A2 homolog piratoxin-1
Similarity search - Component
Biological speciesBothrops pirajai (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.647 Å
AuthorsFernandes, C.A.H. / Fontes, M.R.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2009/10905-5 Brazil
Sao Paulo Research Foundation (FAPESP)2014/17864-8 Brazil
Citation
Journal: Plos One / Year: 2015
Title: Structural Basis for the Inhibition of a Phospholipase A2-Like Toxin by Caffeic and Aristolochic Acids.
Authors: Fernandes, C.A. / Cardoso, F.F. / Cavalcante, W.G. / Soares, A.M. / Dal-Pai, M. / Gallacci, M. / Fontes, M.R.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization and preliminary X-ray diffraction analysis of a Lys49-phospholipase A2 complexed with caffeic acid, a molecule with inhibitory properties against snake venoms.
Authors: Shimabuku, P.S. / Fernandes, C.A. / Magro, A.J. / Costa, T.R. / Soares, A.M. / Fontes, M.R.
History
DepositionMar 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Basic phospholipase A2 homolog piratoxin-1
A: Basic phospholipase A2 homolog piratoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,38810
Polymers27,5082
Non-polymers1,8808
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-11 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.233, 72.082, 44.644
Angle α, β, γ (deg.)90.00, 102.08, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Basic phospholipase A2 homolog piratoxin-1 / svPLA2 homolog / Myotoxin SIV-SP5 / Piratoxin-I / PrTX-I


Mass: 13754.101 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bothrops pirajai (snake) / References: UniProt: P58399
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Chemical
ChemComp-DHC / CAFFEIC ACID / 3,4-DIHYDROXYCINNAMIC ACID


Mass: 180.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H8O4
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.1 / Details: PEG4000, Tris HCl pH 8.1, lithium sulfate.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4568 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4568 Å / Relative weight: 1
ReflectionResolution: 1.6468→40 Å / Num. all: 27814 / Num. obs: 29444 / % possible obs: 94.47 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 27.4
Reflection shellResolution: 1.6468→1.706 Å / Num. measured obs: 2724

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IQ3

3iq3


Resolution: 1.647→37.341 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 24.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2287 1414 5.09 %
Rwork0.1823 --
obs0.1847 27807 94.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.647→37.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 108 289 2246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072004
X-RAY DIFFRACTIONf_angle_d1.1782659
X-RAY DIFFRACTIONf_dihedral_angle_d16.332765
X-RAY DIFFRACTIONf_chiral_restr0.079266
X-RAY DIFFRACTIONf_plane_restr0.006337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6468-1.70560.31091300.27062588X-RAY DIFFRACTION92
1.7056-1.77390.32371420.26212637X-RAY DIFFRACTION95
1.7739-1.85460.29741470.22932684X-RAY DIFFRACTION96
1.8546-1.95240.25561450.19592699X-RAY DIFFRACTION96
1.9524-2.07470.24851440.18432682X-RAY DIFFRACTION97
2.0747-2.23490.24271530.16442695X-RAY DIFFRACTION97
2.2349-2.45980.21961160.17012711X-RAY DIFFRACTION96
2.4598-2.81560.23151490.18372649X-RAY DIFFRACTION94
2.8156-3.54690.21831400.17552619X-RAY DIFFRACTION94
3.5469-37.35060.19611480.17052429X-RAY DIFFRACTION86
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)
12.98250.59250.96923.37891.41923.0165-0.13350.22650.0079-0.28590.1087-0.1342-0.21690.0847-0.02780.17340.00840.01570.1986-0.00110.2223-8.5779-20.82546.0161
20.746-0.2991-0.99426.76551.99323.60890.12490.05940.1128-0.0890.262-0.3663-0.09680.5557-0.13680.21310.02070.00750.2962-0.03630.2428-0.2068-26.76456.6488
33.62841.7075-0.90192.9423-0.34392.6859-0.00120.26780.0557-0.25080.00490.23260.2061-0.2228-0.01480.24930.0073-0.02310.1996-0.02130.2249-7.7444-38.83319.2466
42.0238-1.08480.8232.4216-0.2981.66480.01920.1153-0.1374-0.12910.04840.3389-0.0328-0.263-0.05290.141-0.0071-0.01050.1999-0.01310.217-17.0014-29.51417.1644
55.8770.3421.5370.4561-0.38841.102-0.0388-0.31320.49120.0272-0.25460.4402-0.1182-0.38270.32150.14120.014-0.03030.2341-0.04210.2841-15.6001-13.472710.9792
66.638-3.02893.69292.5668-1.19512.9721-0.1185-0.2874-0.25450.090.14590.2314-0.1413-0.25680.00650.2008-0.01010.03170.1989-0.010.2241-13.5139-24.576712.8778
73.2869-0.767-0.39835.6440.84675.509-0.21850.2065-0.1243-0.2659-0.00240.03570.49210.28830.21590.20550.03880.04550.2054-0.01710.22870.2763-39.67578.3055
82.1546-1.80862.42098.0687-2.63722.8571-0.1508-0.1915-0.84980.45490.30811.14340.0928-0.7750.05080.4222-0.00630.12370.35540.02350.4791-15.5965-44.849812.0573
94.55270.7576-1.44922.7374-0.31652.787-0.14530.2081-0.23950.29110.0596-0.13120.24220.1084-0.0410.1306-0.014-0.00320.2003-0.0050.1927-3.3783-43.5782-9.3095
101.7546-0.79-0.57085.43071.91524.3712-0.039-0.5286-0.39420.22470.2644-0.34060.22630.1194-0.03530.18470.0046-0.04460.2747-0.02350.22393.3639-37.7388-4.8728
112.7876-0.32460.47952.2878-0.28971.885-0.0876-0.18360.34340.1990.06670.0981-0.2042-0.1841-0.00880.2535-0.0032-0.0060.1961-0.02180.2192-2.3946-25.894-10.1097
127.88561.81920.74373.5206-0.17452.6389-0.27310.27240.2362-0.24990.22930.3902-0.3054-0.39540.04320.16250.0202-0.02150.2167-0.00620.2236-6.2086-30.4954-16.0573
131.82990.5132-0.77793.59991.01473.3008-0.0092-0.22020.14290.40220.21810.4554-0.139-0.4549-0.26870.2485-0.05630.06560.4203-0.02980.3688-16.516-41.4193-10.5813
149.5316-2.25550.59751.1767-0.71271.09420.29450.5589-0.6604-0.1636-0.21420.4240.2673-0.28190.0090.1798-0.0128-0.02460.2525-0.0460.296-6.8553-50.6221-17.206
159.71912.4366-0.09911.64570.18710.9931-0.01450.21380.14470.02710.04330.18290.0647-0.1919-0.00210.17-0.02140.00010.25470.00190.2318-7.0024-40.752-17.5234
161.8405-0.0156-0.7944.32772.26335.4772-0.0974-0.59040.03570.45460.0592-0.2247-0.01670.80290.0410.1486-0.0458-0.06020.25760.00270.18088.7725-29.9771-10.439
173.6524-1.1143-0.19622.66920.81852.6185-0.3945-0.17550.32840.58470.17830.4862-0.55330.0758-0.06890.4451-0.0004-0.08580.1976-0.05910.33720.814-23.0517-3.3241
180.91170.8828-0.98885.0316-0.33811.1757-0.22660.35430.4116-0.2280.45240.724-0.69950.3530.15870.4238-0.0652-0.02440.30080.1250.4775-7.2558-19.3694-16.3493
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 13 )
2X-RAY DIFFRACTION2chain 'B' and (resid 14 through 21 )
3X-RAY DIFFRACTION3chain 'B' and (resid 22 through 38 )
4X-RAY DIFFRACTION4chain 'B' and (resid 39 through 65 )
5X-RAY DIFFRACTION5chain 'B' and (resid 66 through 79 )
6X-RAY DIFFRACTION6chain 'B' and (resid 80 through 102 )
7X-RAY DIFFRACTION7chain 'B' and (resid 103 through 114 )
8X-RAY DIFFRACTION8chain 'B' and (resid 115 through 121 )
9X-RAY DIFFRACTION9chain 'A' and (resid 1 through 13 )
10X-RAY DIFFRACTION10chain 'A' and (resid 14 through 21 )
11X-RAY DIFFRACTION11chain 'A' and (resid 22 through 38 )
12X-RAY DIFFRACTION12chain 'A' and (resid 39 through 53 )
13X-RAY DIFFRACTION13chain 'A' and (resid 54 through 65 )
14X-RAY DIFFRACTION14chain 'A' and (resid 66 through 79 )
15X-RAY DIFFRACTION15chain 'A' and (resid 80 through 98 )
16X-RAY DIFFRACTION16chain 'A' and (resid 99 through 107 )
17X-RAY DIFFRACTION17chain 'A' and (resid 108 through 114 )
18X-RAY DIFFRACTION18chain 'A' and (resid 115 through 121 )

+
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