[English] 日本語
Yorodumi
- PDB-3t0r: Crystal Structure of MjTX-I, a myotoxic Lys49-phospholipase A2 fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3t0r
TitleCrystal Structure of MjTX-I, a myotoxic Lys49-phospholipase A2 from Bothrops moojeni
ComponentsPhospholipase A2 homolog 1
KeywordsTOXIN / Lys49-phospholipase A2 / Myotoxin / Venom Glands
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 / Phospholipase A2 domain ...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 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Basic phospholipase A2 homolog MjTX-I
Similarity search - Component
Biological speciesBothrops moojeni (Brazilian lancehead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsSalvador, G.H.M. / Marchi-Salvador, D.P. / Fontes, M.R.M.
CitationJournal: To be Published
Title: Crystal Structure of MjTX-I, a myotoxic Lys49-phospholipase A2 from Bothrops moojeni
Authors: Salvador, G.H.M. / Marchi-Salvador, D.P. / Fontes, M.R.M.
History
DepositionJul 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phospholipase A2 homolog 1
B: Phospholipase A2 homolog 1
C: Phospholipase A2 homolog 1
D: Phospholipase A2 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4115
Polymers55,0564
Non-polymers3541
Water2,036113
1
A: Phospholipase A2 homolog 1
B: Phospholipase A2 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8833
Polymers27,5282
Non-polymers3541
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Phospholipase A2 homolog 1
D: Phospholipase A2 homolog 1


Theoretical massNumber of molelcules
Total (without water)27,5282
Polymers27,5282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Phospholipase A2 homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1192
Polymers13,7641
Non-polymers3541
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Phospholipase A2 homolog 1


Theoretical massNumber of molelcules
Total (without water)13,7641
Polymers13,7641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Phospholipase A2 homolog 1


Theoretical massNumber of molelcules
Total (without water)13,7641
Polymers13,7641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Phospholipase A2 homolog 1


Theoretical massNumber of molelcules
Total (without water)13,7641
Polymers13,7641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.593, 125.848, 65.327
Angle α, β, γ (deg.)90.00, 105.91, 90.00
Int Tables number5
Space group name H-MC121
DetailsAccording to Small Angle X-ray Scattering experiments

-
Components

#1: Protein
Phospholipase A2 homolog 1 / MjTX-I / Myotoxin I


Mass: 13764.075 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bothrops moojeni (Brazilian lancehead) / References: UniProt: P82114, phospholipase A2
#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.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 32% (w/v) PEG 4000; 0.1 M Tris HCl; 0.15 M Magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
PH range: 8,5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.421 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 20, 2010 / Details: Mirrors
RadiationMonochromator: Si curved crystal asymmetrically-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.421 Å / Relative weight: 1
ReflectionResolution: 2.49→33.44 Å / Num. all: 15300 / Num. obs: 15300 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 43.016 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 20.64
Reflection shellResolution: 2.49→2.55 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.69 / Num. unique all: 1541 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QLL

1qll


Resolution: 2.49→33.44 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.897 / SU B: 26.875 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26671 759 5 %RANDOM
Rwork0.23123 ---
obs0.23297 14529 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.016 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.05 Å2
2--0.05 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.49→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3547 0 24 113 3684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223654
X-RAY DIFFRACTIONr_angle_refined_deg2.1511.9764930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7595469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.34724.228149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.06115609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.3631523
X-RAY DIFFRACTIONr_chiral_restr0.1350.2520
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212724
X-RAY DIFFRACTIONr_mcbond_it2.1531.52349
X-RAY DIFFRACTIONr_mcangle_it3.86723708
X-RAY DIFFRACTIONr_scbond_it4.54531305
X-RAY DIFFRACTIONr_scangle_it6.9534.51222
X-RAY DIFFRACTIONr_rigid_bond_restr2.59933654
LS refinement shellResolution: 2.49→2.554 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 54 -
Rwork0.3 1010 -
obs--92.84 %
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)
10.87610.54920.57242.09070.86370.5244-0.074-0.03930.09650.03970.0596-0.1054-0.0384-0.02120.01450.08540.02340.0090.13820.01910.156936.111963.314132.7092
20.3150.8960.26583.44060.12161.09690.03470.081-0.09940.27220.112-0.19780.014-0.0273-0.14670.0657-0.00950.03650.16660.05230.191433.102731.437828.2515
30.846-0.4488-0.06294.11010.85232.8526-0.0735-0.08250.1065-0.01370.28330.06070.12450.104-0.20980.09980.1018-0.02360.1497-0.00880.084316.787477.31530.7287
41.0233-0.47250.54354.30311.27922.4087-0.1879-0.1217-0.17660.7840.43780.13740.0783-0.2436-0.24980.25040.1510.0960.20120.12240.096216.849146.0666-2.0331
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 133
2X-RAY DIFFRACTION2B1 - 133
3X-RAY DIFFRACTION3C1 - 133
4X-RAY DIFFRACTION4D1 - 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://pdbjlvh1.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