[English] 日本語
Yorodumi
- PDB-8ofd: Crystal structure of beta-conglutin from Lupinus albus refined to... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ofd
TitleCrystal structure of beta-conglutin from Lupinus albus refined to 2.81 A
ComponentsConglutin beta 1
KeywordsALLERGEN / beta-conglutin / Lup an 1 / seed storage protein
Function / homologyCupin / Cupin 1 / Cupin / nutrient reservoir activity / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / ACETATE ION / : / Conglutin beta 1
Function and homology information
Biological speciesLupinus albus (white lupine)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsDolot, R.M. / O'Sullivan, C.K. / Jauset-Rubio, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: First crystal structure of beta-conglutin, a major lupin allergen from Lupinus albus seeds
Authors: Dolot, R.M. / O'Sullivan, C.K. / Jauset-Rubio, M.
History
DepositionMar 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Conglutin beta 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1514
Polymers49,0301
Non-polymers1213
Water1,47782
1
A: Conglutin beta 1
hetero molecules

A: Conglutin beta 1
hetero molecules

A: Conglutin beta 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,45312
Polymers147,0903
Non-polymers3639
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Unit cell
Length a, b, c (Å)166.630, 166.630, 40.098
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-602-

NA

-
Components

#1: Protein Conglutin beta 1 / Protein Lup-1


Mass: 49029.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: 1-30 - signal protein (not present) 31-108 - propeptide (not present) 109-531 - conglutin beta 1. Residues 408-415 and 518-531 not included. Residue 176 changed from L to I based on experimental data.
Source: (natural) Lupinus albus (white lupine) / References: UniProt: Q53HY0
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 40% (v/v) Tacsimate pH 7.0, 50 mM HEPES pH 7.0, 2 mM Spermine, and 2 mM Hexaamine cobalt (III)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU PhotonJet-S / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Apr 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.81→21.77 Å / Num. obs: 15700 / % possible obs: 99.7 % / Redundancy: 7.8 % / Biso Wilson estimate: 55 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.064 / Rrim(I) all: 0.182 / Χ2: 0.93 / Net I/σ(I): 9.1
Reflection shellResolution: 2.81→2.96 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.001 / Mean I/σ(I) obs: 2 / Num. unique obs: 2263 / CC1/2: 0.657 / Rpim(I) all: 0.366 / Rrim(I) all: 1.067 / Χ2: 0.92 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
CrysalisPro1.171.41.100data reduction
Aimless0.7.9data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→21.767 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.844 / WRfactor Rfree: 0.258 / WRfactor Rwork: 0.192 / SU B: 14.27 / SU ML: 0.303 / Average fsc free: 0.9384 / Average fsc work: 0.9696 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.08
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2772 774 4.934 %
Rwork0.204 14912 -
all0.208 --
obs-15686 99.771 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 62.202 Å2
Baniso -1Baniso -2Baniso -3
1-0.895 Å20 Å20 Å2
2--0.895 Å20 Å2
3----1.79 Å2
Refinement stepCycle: LAST / Resolution: 2.81→21.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3281 0 6 82 3369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123367
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163139
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.6574553
X-RAY DIFFRACTIONr_angle_other_deg0.4391.577195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7485403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.377533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.80410586
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.93210199
X-RAY DIFFRACTIONr_chiral_restr0.0580.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02874
X-RAY DIFFRACTIONr_nbd_refined0.2280.2803
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2180.23373
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21613
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22074
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2141
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0510.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2210.250
X-RAY DIFFRACTIONr_nbd_other0.2420.2162
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.250.29
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1590.21
X-RAY DIFFRACTIONr_mcbond_it4.9556.2111613
X-RAY DIFFRACTIONr_mcbond_other4.9416.2121612
X-RAY DIFFRACTIONr_mcangle_it7.67311.1422015
X-RAY DIFFRACTIONr_mcangle_other7.67211.1442016
X-RAY DIFFRACTIONr_scbond_it5.086.6591754
X-RAY DIFFRACTIONr_scbond_other5.0796.6581755
X-RAY DIFFRACTIONr_scangle_it7.90412.0032538
X-RAY DIFFRACTIONr_scangle_other7.90312.0022539
X-RAY DIFFRACTIONr_lrange_it12.23873.0263888
X-RAY DIFFRACTIONr_lrange_other12.24373.0873883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.8820.442570.2431077X-RAY DIFFRACTION99.561
2.882-2.9590.333780.2311009X-RAY DIFFRACTION100
2.959-3.0430.412450.2181037X-RAY DIFFRACTION99.9077
3.043-3.1350.265400.2271017X-RAY DIFFRACTION99.9055
3.135-3.2360.327510.212945X-RAY DIFFRACTION100
3.236-3.3470.29510.187963X-RAY DIFFRACTION99.9015
3.347-3.470.271420.197879X-RAY DIFFRACTION100
3.47-3.6080.256440.208899X-RAY DIFFRACTION100
3.608-3.7630.236380.196820X-RAY DIFFRACTION100
3.763-3.9410.314440.199817X-RAY DIFFRACTION99.884
3.941-4.1470.262500.195745X-RAY DIFFRACTION100
4.147-4.3880.266350.176742X-RAY DIFFRACTION100
4.388-4.6780.218460.161669X-RAY DIFFRACTION100
4.678-5.0330.233240.181679X-RAY DIFFRACTION100
5.033-5.4850.206370.199562X-RAY DIFFRACTION100
5.485-6.0840.229150.229570X-RAY DIFFRACTION100
6.084-6.9350.321320.228483X-RAY DIFFRACTION100
6.935-8.2860.319140.223437X-RAY DIFFRACTION99.3392
8.286-10.9520.249130.221342X-RAY DIFFRACTION99.162
10.952-21.7670.346180.311220X-RAY DIFFRACTION91.8919

+
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