[English] 日本語
Yorodumi
- PDB-3jql: Crystal Structure of the Complex Formed Between Phospholipase A2 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jql
TitleCrystal Structure of the Complex Formed Between Phospholipase A2 and a Hexapeptide Fragment of Amyloid Beta Peptide, Lys-Leu-Val-Phe-Phe-Ala at 1.2 A Resolution
Components
  • Acidic phospholipase A2 3 (Fragment)
  • Amyloid Beta PeptideAmyloid beta
KeywordsHYDROLASE / PHOSPHOLIPASE A2 / HEXAPEPTIDE / AMYLOID BETA / Disulfide bond / Lipid degradation / Metal-binding / Secreted
Function / homology
Function and homology information


phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / 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
Acidic phospholipase A2 3
Similarity search - Component
Biological speciesNaja sagittifera (cobra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsMirza, Z. / Vikram, G. / Singh, N. / Sinha, M. / Sharma, S. / Srinivasan, A. / Kaur, P. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal Structure of the Complex Formed Between Phospholipase A2 and a Hexapeptide Fragment of Amyloid Beta Peptide, Lys-Leu-Val-Phe-Phe-Ala at 1.2 A Resolution
Authors: Mirza, Z. / Vikram, G. / Singh, N. / Sinha, M. / Sharma, S. / Srinivasan, A. / Kaur, P. / Singh, T.P.
History
DepositionSep 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_nat / pdbx_entity_src_syn / pdbx_initial_refinement_model / struct_ref / struct_ref_seq / 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 / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_nat.common_name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref_seq_dif.details / _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: Acidic phospholipase A2 3 (Fragment)
B: Amyloid Beta Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8943
Polymers13,8532
Non-polymers401
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-19 kcal/mol
Surface area6820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.023, 42.023, 64.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Acidic phospholipase A2 3 (Fragment)


Mass: 13128.515 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja sagittifera (cobra) / References: UniProt: P60045
#2: Protein/peptide Amyloid Beta Peptide / Amyloid beta


Mass: 724.909 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide synthesis
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIN CHAIN A, RESIDUE NUMBER 16 IS SIMPLY SKIPPED. THE AUTHORS BELIEVE THAT THE SEQRES IS CORRECT AND ...IN CHAIN A, RESIDUE NUMBER 16 IS SIMPLY SKIPPED. THE AUTHORS BELIEVE THAT THE SEQRES IS CORRECT AND THESE MUTATIONS ARE PRESENT IN THE DEPOSITED SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: calcium chloride, sodium phosphate, PH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 30, 2009 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.2→42 Å / Num. all: 34924 / Num. obs: 34924 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.036 / Net I/σ(I): 7.9
Reflection shellResolution: 1.2→1.22 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.122 / % possible all: 94.6

-
Processing

Software
NameVersionClassification
DENZOdata reduction
MOLREPphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MF4

1mf4


Resolution: 1.2→42 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.294 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.052 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19284 1695 5.1 %RANDOM
Rwork0.18076 ---
obs0.18662 31789 96 %-
all-34924 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.326 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.2→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms960 0 1 149 1110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022986
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.9291337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2365122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32824.70651
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80915146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.568155
X-RAY DIFFRACTIONr_chiral_restr0.0810.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02775
X-RAY DIFFRACTIONr_nbd_refined0.2140.2473
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2664
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0810.2113
X-RAY DIFFRACTIONr_metal_ion_refined0.0340.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0770.224
X-RAY DIFFRACTIONr_mcbond_it0.8331.5635
X-RAY DIFFRACTIONr_mcangle_it1.3022978
X-RAY DIFFRACTIONr_scbond_it1.9073410
X-RAY DIFFRACTIONr_scangle_it2.5014.5359
X-RAY DIFFRACTIONr_rigid_bond_restr1.33731045
X-RAY DIFFRACTIONr_sphericity_free2.1753154
X-RAY DIFFRACTIONr_sphericity_bonded2.363960
LS refinement shellResolution: 1.199→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 104 -
Rwork0.229 2300 -
obs--94.57 %

+
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