[English] 日本語
Yorodumi
- PDB-9die: Structure of phospholipase D BetaIB1i from Sicarius terrosus veno... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9die
TitleStructure of phospholipase D BetaIB1i from Sicarius terrosus venom, H47N mutant bound to product and substrate sphingolipids at 1.85 A resolution
ComponentsDermonecrotic toxin StSicTox-betaIB1i
KeywordsLYASE / toxin sphingolipid spider venom interfacial binding site
Function / homology
Function and homology information


phosphoric diester hydrolase activity / lipid catabolic process / toxin activity / Lyases; Phosphorus-oxygen lyases / killing of cells of another organism / lyase activity / extracellular region / metal ion binding
Similarity search - Function
Glycerophosphoryl diester phosphodiesterase family / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily
Similarity search - Domain/homology
: / : / Dermonecrotic toxin StSicTox-betaIB1i
Similarity search - Component
Biological speciesSicarius terrosus (spider)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSundman, A.K. / Montfort, W.R. / Binford, G.J. / Cordes, M.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1808716 United States
CitationJournal: To Be Published
Title: Structure of phospholipase D BetaIB1i from Sicarius terrosus venom, H47N mutant bound to product and substrate sphingolipids at 1.85 A resolution
Authors: Sundman, A.K. / Montfort, W.R. / Binford, G.J. / Cordes, M.H.
History
DepositionSep 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dermonecrotic toxin StSicTox-betaIB1i
B: Dermonecrotic toxin StSicTox-betaIB1i
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,32416
Polymers68,5252
Non-polymers3,80014
Water15,925884
1
A: Dermonecrotic toxin StSicTox-betaIB1i
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2809
Polymers34,2621
Non-polymers2,0188
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dermonecrotic toxin StSicTox-betaIB1i
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0447
Polymers34,2621
Non-polymers1,7826
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.999, 105.327, 108.406
Angle α, β, γ (deg.)90.00, 93.83, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-662-

HOH

21B-519-

HOH

31B-680-

HOH

41B-833-

HOH

51B-841-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Dermonecrotic toxin StSicTox-betaIB1i / Phospholipase D / PLD / Sphingomyelin phosphodiesterase D / SMD / SMase D / Sphingomyelinase D


Mass: 34262.332 Da / Num. of mol.: 2 / Mutation: H47N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sicarius terrosus (spider) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0D4WV12, Lyases; Phosphorus-oxygen lyases

-
Non-polymers , 6 types, 898 molecules

#2: Chemical
ChemComp-A1A43 / 2-aminoethyl (2S,3R,4E)-2-dodecanamido-3-hydroxyheptadec-4-en-1-yl hydrogen (S)-phosphate


Mass: 590.815 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H63N2O6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1A44 / N-{(2S,4R,5S)-2-hydroxy-2-oxo-4-[(1E,7Z)-tetradeca-1,7-dien-1-yl]-1,3,2lambda~5~-dioxaphosphinan-5-yl}dodecanamide


Mass: 529.732 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H56NO5P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 884 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1 mg/mL protein, 0.4 mM ceramidephosphoethanolamine, 5 mg/mL CHAPS, 8.25% methyl-2,4-pentanediol, 75 mM sodium chloride, 27.5 mM sodium acetate (pH 4.6), ~30 mM Tris, 1 mM magnesium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: May 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.85→24.43 Å / Num. obs: 76317 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.167 / Net I/σ(I): 9.6
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 1.836 / Num. unique obs: 4518

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimless0.7.9data scaling
PROTEUM22021.10-0data reduction
MOLREP11.9.12phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→24.43 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.946 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1674 3751 4.9 %RANDOM
Rwork0.11878 ---
obs0.12119 72553 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.937 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0 Å2-0.19 Å2
2---0.14 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.85→24.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 254 884 5614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125103
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164893
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.8656912
X-RAY DIFFRACTIONr_angle_other_deg0.6011.79211365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7045634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.543556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01810875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2727
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026081
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021203
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5211.4712341
X-RAY DIFFRACTIONr_mcbond_other3.5171.4712341
X-RAY DIFFRACTIONr_mcangle_it5.3042.6392956
X-RAY DIFFRACTIONr_mcangle_other5.3052.642957
X-RAY DIFFRACTIONr_scbond_it6.8042.1222762
X-RAY DIFFRACTIONr_scbond_other6.8032.1242763
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.4233.6333927
X-RAY DIFFRACTIONr_long_range_B_refined19.16618.136390
X-RAY DIFFRACTIONr_long_range_B_other18.14317.676232
X-RAY DIFFRACTIONr_rigid_bond_restr3.37639996
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 269 -
Rwork0.321 5355 -
obs--99.88 %

+
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