[English] 日本語
Yorodumi
- PDB-1m8t: Structure of an acidic Phospholipase A2 from the venom of Ophioph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m8t
TitleStructure of an acidic Phospholipase A2 from the venom of Ophiophagus hannah at 2.1 resolution from a hemihedrally twinned crystal form
ComponentsPhospholipase a2
KeywordsHYDROLASE / phospholipase a2 structure / twinned crystal / alpha / beta
Function / homology
Function and homology information


phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity / phospholipase A2 / arachidonate 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
HEXANE-1,6-DIOL / Acidic phospholipase A2 2
Similarity search - Component
Biological speciesOphiophagus hannah (king cobra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXu, S. / Gu, L. / Wang, Q. / Shu, Y. / Lin, Z.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of a king cobra phospholipase A2 determined from a hemihedrally twinned crystal.
Authors: Xu, S. / Gu, L. / Wang, Q. / Shu, Y. / Song, S. / Lin, Z.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Preliminary crystallographic study of an acidic phospholipase A2 from Ophiophagus hannah (king cobra)
Authors: Xu, S. / Gu, L. / Wang, Q. / Shu, Y. / Lin, Z.
History
DepositionJul 26, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_asym_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_asym_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_conn.ptnr2_label_seq_id / _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
B: Phospholipase a2
C: Phospholipase a2
D: Phospholipase a2
E: Phospholipase a2
F: Phospholipase a2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,62622
Polymers79,2046
Non-polymers1,42216
Water15,403855
1
A: Phospholipase a2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7136
Polymers13,2011
Non-polymers5135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phospholipase a2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3593
Polymers13,2011
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phospholipase a2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4774
Polymers13,2011
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phospholipase a2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5955
Polymers13,2011
Non-polymers3954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Phospholipase a2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2412
Polymers13,2011
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Phospholipase a2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2412
Polymers13,2011
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.06, 98.06, 132.39
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein
Phospholipase a2


Mass: 13200.592 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Ophiophagus hannah (king cobra) / Secretion: venom / References: UniProt: Q9DF33, phospholipase A2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 855 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 3.4M 1,6-hexanediol, 0.2M magnesium chloride, 0.1M tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
23.4 M1,6-hexanediol1drop
30.2 M1dropMgCl2
40.1 MTris-HCl1droppH8.5
50.1 MTris-HCl1reservoirpH8.5
66 M1,6-hexanediol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jan 23, 2002 / Details: Osmic Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→17 Å / Num. all: 41966 / Num. obs: 41966 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 16.1 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 38.1
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 14 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 7.4 / Num. unique all: 4153 / % possible all: 98.8
Reflection
*PLUS
Lowest resolution: 17 Å / Num. measured all: 1527037
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 98.8 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1POA

1poa


Resolution: 2.1→16.99 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: TWINNED R VALUE (WORKING SET): 0.195, TWINNED FREE R VALUE: 0.215; TWINNED BIN R VALUE (WORKING SET): 0.285, TWINNED BIN FREE R VALUE: 0.248
RfactorNum. reflection% reflection
Rfree0.213 2026 4.8 %
Rwork0.192 --
all0.196 41938 -
obs-41938 99.9 %
Solvent computationSolvent model: FLAT MODEL / Bsol: 95.581 Å2 / ksol: 0.352776 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.98 Å21.14 Å20 Å2
2---3.98 Å20 Å2
3---7.97 Å2
Refinement stepCycle: LAST / Resolution: 2.1→16.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5473 0 86 855 6414
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.922
X-RAY DIFFRACTIONc_scbond_it1.492
X-RAY DIFFRACTIONc_scangle_it2.242.5
LS refinement shellResolution: 2.1→2.23 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 347 5 %
Rwork0.237 --
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4BBO.PARAMBBO.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 17 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.47
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87

+
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://pdbjlc1.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