[English] 日本語
Yorodumi
- PDB-6tmy: Crystal structure of isoform CBd of the basic phospholipase A2 su... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tmy
TitleCrystal structure of isoform CBd of the basic phospholipase A2 subunit of crotoxin from Crotalus durissus terrificus
ComponentsPhospholipase A2 crotoxin basic subunit CBc
KeywordsHYDROLASE / crotoxin / CB isoforms / presynaptic phospholipase A2
Function / homology
Function and homology information


envenomation resulting in induction of edema in another organism / envenomation resulting in muscle damage in another organism / envenomation resulting in myocyte killing in another organism / envenomation resulting in positive regulation of platelet aggregation in another organism / ion channel regulator activity / phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process ...envenomation resulting in induction of edema in another organism / envenomation resulting in muscle damage in another organism / envenomation resulting in myocyte killing in another organism / envenomation resulting in positive regulation of platelet aggregation in another organism / ion channel regulator activity / 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 domain superfamily
Similarity search - Domain/homology
Phospholipase A2 crotoxin basic subunit CBc
Similarity search - Component
Biological speciesCrotalus durissus terrificus (tropical rattlesnake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNemecz, D. / Ostrowski, M. / Saul, F.A. / Faure, G.
Funding support Poland, 1items
OrganizationGrant numberCountry
Other governmentPOKL.04.01.01-00-081/10 Poland
CitationJournal: Molecules / Year: 2020
Title: Crystal Structure of Isoform CBd of the Basic Phospholipase A 2 Subunit of Crotoxin: Description of the Structural Framework of CB for Interaction with Protein Targets.
Authors: Nemecz, D. / Ostrowski, M. / Ravatin, M. / Saul, F. / Faure, G.
History
DepositionDec 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2Jan 24, 2024Group: 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 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phospholipase A2 crotoxin basic subunit CBc
B: Phospholipase A2 crotoxin basic subunit CBc
C: Phospholipase A2 crotoxin basic subunit CBc
D: Phospholipase A2 crotoxin basic subunit CBc
E: Phospholipase A2 crotoxin basic subunit CBc
F: Phospholipase A2 crotoxin basic subunit CBc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,73238
Polymers85,6836
Non-polymers3,04932
Water14,628812
1
A: Phospholipase A2 crotoxin basic subunit CBc
B: Phospholipase A2 crotoxin basic subunit CBc
hetero molecules

E: Phospholipase A2 crotoxin basic subunit CBc
hetero molecules

C: Phospholipase A2 crotoxin basic subunit CBc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,23126
Polymers57,1224
Non-polymers2,10922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation4_557-x+1/2,y+1/2,-z+21
Buried area9730 Å2
ΔGint-129 kcal/mol
Surface area23920 Å2
MethodPISA
2
F: Phospholipase A2 crotoxin basic subunit CBc
hetero molecules

F: Phospholipase A2 crotoxin basic subunit CBc
hetero molecules

D: Phospholipase A2 crotoxin basic subunit CBc
hetero molecules

D: Phospholipase A2 crotoxin basic subunit CBc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,00124
Polymers57,1224
Non-polymers1,88020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558-x,y,-z+31
crystal symmetry operation3_455x-1/2,y+1/2,z1
crystal symmetry operation4_558-x+1/2,y+1/2,-z+31
Buried area9070 Å2
ΔGint-125 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.626, 75.592, 109.012
Angle α, β, γ (deg.)90.000, 121.850, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-317-

HOH

-
Components

#1: Protein
Phospholipase A2 crotoxin basic subunit CBc / svPLA2 / Phosphatidylcholine 2-acylhydrolase


Mass: 14280.483 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Crotalus durissus terrificus (tropical rattlesnake)
References: UniProt: P62022, phospholipase A2
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 812 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 400, 0.1M NACL, 0.18M SODIUM ACETATE, 0.1M TRIS

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.8→47.5 Å / Num. obs: 94489 / % possible obs: 98.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 33.29 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4708 / % possible all: 97

-
Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R0L POLYPEPTIDE CHAIN D
Resolution: 1.8→47.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.118 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1857 1.97 %RANDOM
Rwork0.192 ---
obs0.192 94480 98.7 %-
Displacement parametersBiso max: 125.64 Å2 / Biso mean: 37.38 Å2 / Biso min: 16.73 Å2
Baniso -1Baniso -2Baniso -3
1-4.169 Å20 Å2-4.76 Å2
2--0.3929 Å20 Å2
3----4.5619 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: final / Resolution: 1.8→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5879 0 149 812 6840
Biso mean--52.39 45.25 -
Num. residues----732
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2154SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1019HARMONIC5
X-RAY DIFFRACTIONt_it6221HARMONIC20
X-RAY DIFFRACTIONt_nbd9SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion739SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7444SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6221HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8351HARMONIC20.88
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion14.72
LS refinement shellResolution: 1.8→1.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.35 28 1.48 %
Rwork0.2609 1862 -
all0.2623 1890 -
obs--96.35 %

+
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