[English] 日本語
Yorodumi
- PDB-4bkd: Crystal Structure of an unusually linked dimeric variant of Bet v... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bkd
TitleCrystal Structure of an unusually linked dimeric variant of Bet v 1 (b)
ComponentsMAJOR POLLEN ALLERGEN BET V 1-A
KeywordsALLERGEN / DIMERISATION / POLYSULFIDE
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm
Similarity search - Function
Pathogenesis-related protein Bet v I family / Pathogenesis-related proteins Bet v I family signature. / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / : / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Major pollen allergen Bet v 1-A
Similarity search - Component
Biological speciesBETULA PENDULA (European white birch)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsKofler, S.G. / Brandstetter, H.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Stabilization of the dimeric birch pollen allergen Bet v 1 impacts its immunological properties.
Authors: Kofler, S. / Ackaert, C. / Samonig, M. / Asam, C. / Briza, P. / Horejs-Hoeck, J. / Cabrele, C. / Ferreira, F. / Duschl, A. / Huber, C. / Brandstetter, H.
History
DepositionApr 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 2.0May 8, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other / Polymer sequence
Category: citation / citation_author ...citation / citation_author / entity_poly / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_biol / struct_conn
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_poly.pdbx_seq_one_letter_code_can / _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.2Nov 13, 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: MAJOR POLLEN ALLERGEN BET V 1-A


Theoretical massNumber of molelcules
Total (without water)17,5301
Polymers17,5301
Non-polymers00
Water3,567198
1
A: MAJOR POLLEN ALLERGEN BET V 1-A

A: MAJOR POLLEN ALLERGEN BET V 1-A


Theoretical massNumber of molelcules
Total (without water)35,0602
Polymers35,0602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1750 Å2
ΔGint-4.2 kcal/mol
Surface area19380 Å2
MethodPQS
Unit cell
Length a, b, c (Å)112.925, 44.693, 31.976
Angle α, β, γ (deg.)90.00, 91.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-5-

TQZ

21A-2021-

HOH

31A-2059-

HOH

41A-2063-

HOH

-
Components

#1: Protein MAJOR POLLEN ALLERGEN BET V 1-A / ALLERGEN BET V I-A / BET V 1-A BET V 1


Mass: 17529.822 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BETULA PENDULA (European white birch) / Tissue: POLLEN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15494
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN-TERMINAL METHIONINE PROCESSED.TYROSINE 5 TO CYSTEINE EXCHANGE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.67 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5 / Details: 27 % PEG 3350, 0.1 M NA-ACETATE, PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8865
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8865 Å / Relative weight: 1
ReflectionResolution: 1.17→56.45 Å / Num. obs: 52883 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 17
Reflection shellResolution: 1.17→1.23 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / % possible all: 91.4

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A88

4a88


Resolution: 1.17→56.45 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.425 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. DISORDERED REGION COMPRISING RESIDUES GL60 TO PRO63 WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20172 2687 5.1 %RANDOM
Rwork0.17711 ---
obs0.17842 50194 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.104 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0.67 Å2
2--0.01 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.17→56.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 0 198 1420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021356
X-RAY DIFFRACTIONr_bond_other_d0.0020.02917
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9771851
X-RAY DIFFRACTIONr_angle_other_deg1.29732276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6845185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.29825.51758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.15615237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg33.132154
X-RAY DIFFRACTIONr_chiral_restr0.0840.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211536
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02256
X-RAY DIFFRACTIONr_nbd_refined0.2940.2467
X-RAY DIFFRACTIONr_nbd_other0.2220.2853
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2641
X-RAY DIFFRACTIONr_nbtor_other0.0820.2677
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.255
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1790.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.6571.6421356
X-RAY DIFFRACTIONr_mcbond_other6.5811.681917
X-RAY DIFFRACTIONr_mcangle_it10.2572.4181841
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr15.18332273
X-RAY DIFFRACTIONr_sphericity_free22.82543
X-RAY DIFFRACTIONr_sphericity_bonded10.15452391
LS refinement shellResolution: 1.167→1.198 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 163 -
Rwork0.322 3162 -
obs--84.93 %

+
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