[English] 日本語
Yorodumi
- PDB-1ktj: X-ray Structure Of Der P 2, The Major House Dust Mite Allergen -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ktj
TitleX-ray Structure Of Der P 2, The Major House Dust Mite Allergen
ComponentsALLERGEN DER P 2
KeywordsALLERGEN / asthma / immunoglobulin fold / hydrophobic cavity
Function / homology
Function and homology information


sterol transport / sterol binding / extracellular region
Similarity search - Function
Sterol transport protein NPC2-like / Immunoglobulin-like - #770 / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mite group 2 allergen Der p 2
Similarity search - Component
Biological speciesDermatophagoides pteronyssinus (European house dust mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsDerewenda, U. / Li, J. / Derewenda, Z. / Dauter, Z. / Mueller, G.A. / Rule, G.S. / Benjamin, D.C.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The crystal structure of a major dust mite allergen Der p 2, and its biological implications.
Authors: Derewenda, U. / Li, J. / Derewenda, Z. / Dauter, Z. / Mueller, G.A. / Rule, G.S. / Benjamin, D.C.
History
DepositionJan 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
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_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ALLERGEN DER P 2
B: ALLERGEN DER P 2


Theoretical massNumber of molelcules
Total (without water)28,2312
Polymers28,2312
Non-polymers00
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.692, 108.747, 91.971
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

-
Components

#1: Protein ALLERGEN DER P 2 / DER P II / DPX


Mass: 14115.322 Da / Num. of mol.: 2 / Mutation: D1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dermatophagoides pteronyssinus (European house dust mite)
Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P49278
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

Crystal
ID
1
2
3
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop4.6Peg 4000, sodium citrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2982vapor diffusion, hanging drop5.6ammonium sulfate, sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2983vapor diffusion, hanging drop4.6Peg 4000, sodium citrate, spermine or B-octylglucosite, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
21.8 Mammonium sulfate1reservoir
3100 mMsodium citrate1reservoirpH4.6
435 %(w/v)PEG40001reservoir
55 mMspermine1reservoiror 35%(w/v) beta-octylglucosite
6100 mMsodium citrate1reservoirpH4.6

-
Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9B10.9791, 0.9784, 0.9801
SYNCHROTRONEMBL/DESY, HAMBURG X1120.9
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMay 1, 1999
MARRESEARCH2IMAGE PLATENov 1, 1997
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97841
30.98011
40.91
ReflectionResolution: 2.15→40 Å / Num. all: 19906 / Num. obs: 19747 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 27
Reflection shellResolution: 2.15→2.17 Å / Redundancy: 4 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 3.2 / Num. unique all: 514 / % possible all: 77.3
Reflection shell
*PLUS
% possible obs: 77.3 % / Mean I/σ(I) obs: 3

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.15→20 Å / Isotropic thermal model: isotropic / Cross valid method: R-free / σ(F): 0 / σ(I): 0.5 / Details: final refinement using REFMAC
RfactorNum. reflectionSelection details
Rfree0.27 1947 Random
Rwork0.21 --
all-19729 -
obs-19151 -
Displacement parametersBiso mean: 34.6 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1970 0 0 170 2140
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d0.023
LS refinement shellResolution: 2.153→2.254 Å
RfactorNum. reflection% reflection
Rfree0.299 214 -
Rwork0.225 --
obs-2012 92 %
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.209 / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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