[English] 日本語
Yorodumi
- PDB-3rlh: Crystal structure of a class II phospholipase D from Loxosceles i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rlh
TitleCrystal structure of a class II phospholipase D from Loxosceles intermedia venom
ComponentsDermonecrotic toxin LiSicTox-alphaIA1a
KeywordsHYDROLASE / Class II PLD / TIM beta/alpha-barrel superfamily / PLC-like Phosphodiesterase / Phospholipase-D / Hydrolase.
Function / homology
Function and homology information


phosphoric diester hydrolase activity / lipid catabolic process / Lyases; Phosphorus-oxygen lyases / toxin activity / killing of cells of another organism / lyase activity / extracellular region / metal ion binding
Similarity search - Function
Glycerophosphoryl diester phosphodiesterase family / Phosphatidylinositol (PI) phosphodiesterase / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Dermonecrotic toxin LiSicTox-alphaIA1a
Similarity search - Component
Biological speciesLoxosceles intermedia (spider)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.72 Å
AuthorsGiuseppe, P.O. / Ullah, A. / Veiga, S.S. / Murakami, M.T. / Arni, R.K. / Doherty, D.Z. / Gismene, C. / Bachega, J.F.R. / Chahine, J. / Gonzalez, J.E.H.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2020/08615-8 Brazil
Brazilian National Council for Scientific and Technological Development (CNPq)309940/2019-2 Brazil
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Structure of a novel class II phospholipase D: Catalytic cleft is modified by a disulphide bridge.
Authors: de Giuseppe, P.O. / Ullah, A. / Silva, D.T. / Gremski, L.H. / Wille, A.C. / Chaves Moreira, D. / Ribeiro, A.S. / Chaim, O.M. / Murakami, M.T. / Veiga, S.S. / Arni, R.K.
#1: Journal: To Be Published
Title: Mechanism of phosphate cyclization by Loxoceles intermedia Class II Phospholipase-D
Authors: Gismene, C. / Bachega, J.F.R. / Calil, F.A. / Chahine, J. / Arni, R.K. / Gonzalez, J.E.H.
History
DepositionApr 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 2.0Feb 19, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / audit_author / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / diffrn / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_database_status / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_keywords / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _diffrn.pdbx_serial_crystal_experiment / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _entity_src_gen.pdbx_seq_type / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_contact_author.name_salutation / _pdbx_database_status.SG_entry / _pdbx_database_status.pdb_format_compatible / _pdbx_entry_details.has_ligand_of_interest / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_all / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.occupancy_max / _refine.occupancy_min / _refine.overall_FOM_work_R_set / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.overall_SU_R_Cruickshank_DPI / _refine.overall_SU_R_free / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns.number_all / _reflns.observed_criterion_sigma_I / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_netI_over_sigmaI / _reflns.pdbx_redundancy / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct.pdbx_CASP_flag / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length / _struct_keywords.text / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.details / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id
Description: Ligand identity / Provider: author / Type: Coordinate replacement

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dermonecrotic toxin LiSicTox-alphaIA1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2968
Polymers36,6021
Non-polymers6947
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.810, 49.300, 56.300
Angle α, β, γ (deg.)90.00, 105.83, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Dermonecrotic toxin LiSicTox-alphaIA1a / Dermonecrotic toxin 1 / DT1 / LiRecDT1 / P1 / Phospholipase D / PLD / Sphingomyelin ...Dermonecrotic toxin 1 / DT1 / LiRecDT1 / P1 / Phospholipase D / PLD / Sphingomyelin phosphodiesterase D 1 / SMD 1 / SMase D 1 / Sphingomyelinase D 1


Mass: 36601.926 Da / Num. of mol.: 1 / Fragment: mature phospholipase D / Mutation: E277D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loxosceles intermedia (spider) / Plasmid: pET-14b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS
References: UniProt: P0CE80, Lyases; Phosphorus-oxygen lyases

-
Non-polymers , 6 types, 197 molecules

#2: Chemical ChemComp-A1BTZ / (2r,5r)-5-amino-2-hydroxy-5-(hydroxymethyl)-1,3,2lambda~5~-dioxaphosphinan-2-one


Mass: 183.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10NO5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 1.81 Å3/Da / Density % sol: 32.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Tris-HCl pH 7.5, 40%(v/v) PEG200, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 20, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 1.72→54.165 Å / Num. obs: 28041 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.1
Reflection shellResolution: 1.72→1.81 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 2 / Num. unique obs: 28041 / Rsym value: 0.468 / % possible all: 99.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.87 Å23.74 Å
Translation1.87 Å23.74 Å

-
Processing

Software
NameVersionClassificationNB
PHENIX(1.20.1_4487: ???)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XX1

1xx1


Resolution: 1.72→23.74 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.86 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1971 1408 5.02 %RANDOM
Rwork0.1607 ---
obs0.1626 28026 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.72→23.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 11 190 2421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018
X-RAY DIFFRACTIONf_angle_d1.567
X-RAY DIFFRACTIONf_dihedral_angle_d6.952
X-RAY DIFFRACTIONf_chiral_restr0.12330
X-RAY DIFFRACTIONf_plane_restr0.013406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.780.39211470.28952632X-RAY DIFFRACTION100
1.78-1.850.26911120.23042646X-RAY DIFFRACTION100
1.85-1.940.22231320.18152663X-RAY DIFFRACTION100
1.94-2.040.23531470.15982630X-RAY DIFFRACTION100
2.04-2.170.21161390.15052683X-RAY DIFFRACTION100
2.17-2.330.19941320.14262670X-RAY DIFFRACTION100
2.33-2.570.20631430.15072661X-RAY DIFFRACTION100
2.57-2.940.19311570.15452647X-RAY DIFFRACTION100
2.94-3.70.1871350.15772692X-RAY DIFFRACTION100
3.7-23.740.15151640.14512694X-RAY DIFFRACTION99

+
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