[English] 日本語
Yorodumi
- PDB-1tdv: Non-specific binding to phospholipase A2:Crystal structure of the... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tdv
TitleNon-specific binding to phospholipase A2:Crystal structure of the complex of PLA2 with a designed peptide Tyr-Trp-Ala-Ala-Ala-Ala at 1.7A resolution
Components
  • Phospholipase A2 VRV-PL-VIIIa
  • YWAAAA
KeywordsHYDROLASE / NON-SPECIFIC / YWAAAA COMPLEX / PHOSPHOLIPASE A2
Function / homology
Function and homology information


phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / 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 VRV-PL-VIIIa
Similarity search - Component
Biological speciesDaboia russellii pulchella (snake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSingh, N. / Jabeen, T. / Ethayathulla, A.S. / Somvanshi, R.K. / Sharma, S. / Dey, S. / Perbandt, M. / Betzel, C. / Singh, T.P.
CitationJournal: to be published
Title: Non-specific binding to phospholipase A2:Crystal structure of the complex of PLA2 with a designed peptide Tyr-Trp-Ala-Ala-Ala-Ala at 1.7A resolution
Authors: Singh, N. / Jabeen, T. / Ethayathulla, A.S. / Somvanshi, R.K. / Sharma, S. / Dey, S. / Perbandt, M. / Betzel, C. / Singh, T.P.
History
DepositionMay 24, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phospholipase A2 VRV-PL-VIIIa
B: YWAAAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8588
Polymers14,2812
Non-polymers5766
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.290, 52.290, 47.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

-
Components

#1: Protein Phospholipase A2 VRV-PL-VIIIa / Phospholipase A2


Mass: 13629.767 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Daboia russellii pulchella (snake) / Species: Daboia russellii / Strain: pulchella / References: UniProt: P59071, phospholipase A2
#2: Protein/peptide YWAAAA


Mass: 651.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ywaaaa peptide sequence was chemically synthesized
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M AMMONIUM SULPHATE, 30% PEG, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.806 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 1, 2004 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.806 Å / Relative weight: 1
ReflectionResolution: 1.7→51.99 Å / Num. all: 355374 / Num. obs: 14306 / % possible obs: 100 % / Redundancy: 24.8 % / Biso Wilson estimate: 17.71 Å2 / Rsym value: 0.057 / Net I/σ(I): 27.8
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 6.7 / Num. unique all: 721 / Rsym value: 0.342 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SKG

1skg


Resolution: 1.7→51.99 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.739 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20615 719 5 %RANDOM
Rwork0.17887 ---
all0.1807 14299 --
obs0.18028 13580 99.97 %-
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: 17.915 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.7→51.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 30 147 1167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211036
X-RAY DIFFRACTIONr_bond_other_d0.0010.02859
X-RAY DIFFRACTIONr_angle_refined_deg1.8072.0051388
X-RAY DIFFRACTIONr_angle_other_deg0.97132024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8033118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.45615189
X-RAY DIFFRACTIONr_chiral_restr0.0910.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021078
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02205
X-RAY DIFFRACTIONr_nbd_refined0.4410.3288
X-RAY DIFFRACTIONr_nbd_other0.220.3803
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.5121
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0310.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.312
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.339
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.521
X-RAY DIFFRACTIONr_mcbond_it0.9041.5621
X-RAY DIFFRACTIONr_mcangle_it1.6532975
X-RAY DIFFRACTIONr_scbond_it2.1323415
X-RAY DIFFRACTIONr_scangle_it3.4224.5413
LS refinement shellResolution: 1.7→1.73 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.2 58
Rwork0.162 985

+
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