[English] 日本語
Yorodumi
- PDB-4i4q: BEL beta-trefoil apo crystal form 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i4q
TitleBEL beta-trefoil apo crystal form 3
ComponentsBEL-beta trefoil
KeywordsSUGAR BINDING PROTEIN / lectin / fruiting bodies
Function / homologyRicin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta / BEL-beta trefoil
Function and homology information
Biological speciesBoletus edulis (king bolete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsBovi, M. / Cenci, L. / Perduca, M. / Capaldi, S. / Carrizo, M.E. / Civiero, L. / Chiarelli, L.R. / Galliano, M. / Monaco, H.L.
CitationJournal: Glycobiology / Year: 2013
Title: BEL {beta}-trefoil: A novel lectin with antineoplastic properties in king bolete (Boletus edulis) mushrooms.
Authors: Bovi, M. / Cenci, L. / Perduca, M. / Capaldi, S. / Carrizo, M.E. / Civiero, L. / Chiarelli, L.R. / Galliano, M. / Monaco, H.L.
History
DepositionNov 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: BEL-beta trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8684
Polymers16,5921
Non-polymers2763
Water3,027168
1
A: BEL-beta trefoil
hetero molecules

A: BEL-beta trefoil
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7378
Polymers33,1842
Non-polymers5536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.744, 77.744, 52.772
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-330-

HOH

21A-388-

HOH

-
Components

#1: Protein BEL-beta trefoil


Mass: 16592.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Boletus edulis (king bolete) / References: UniProt: R4GRU4*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate, 0.2 magnesium acetate, 20% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 22, 2011
RadiationMonochromator: Diamond(001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→16.832 Å / Num. all: 29039 / Num. obs: 29039 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 3.9
Reflection shellResolution: 1.51→1.56 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 1.3 / % possible all: 89.5

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4I4P

4i4p


Resolution: 1.51→16.832 Å / SU ML: 0.52 / σ(F): 1.36 / Phase error: 17.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 1467 5.06 %RANDOM
Rwork0.1879 ---
obs0.1892 28987 99.34 %-
all-28987 --
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.05 Å2 / ksol: 0.6 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1529 Å20 Å20 Å2
2---0.1529 Å2-0 Å2
3---0.3059 Å2
Refinement stepCycle: LAST / Resolution: 1.51→16.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 18 168 1365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061237
X-RAY DIFFRACTIONf_angle_d1.1271685
X-RAY DIFFRACTIONf_dihedral_angle_d10.921441
X-RAY DIFFRACTIONf_chiral_restr0.081171
X-RAY DIFFRACTIONf_plane_restr0.006225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.5640.43171380.39972605X-RAY DIFFRACTION95
1.564-1.62650.29271420.27492729X-RAY DIFFRACTION100
1.6265-1.70050.21241580.20752736X-RAY DIFFRACTION100
1.7005-1.790.19251290.16532747X-RAY DIFFRACTION100
1.79-1.90210.20681480.14852763X-RAY DIFFRACTION100
1.9021-2.04870.17551430.15262763X-RAY DIFFRACTION100
2.0487-2.25440.16961650.15512729X-RAY DIFFRACTION100
2.2544-2.57960.18621520.17152778X-RAY DIFFRACTION100
2.5796-3.24620.17431500.16992813X-RAY DIFFRACTION100
3.2462-16.83310.27661420.21092857X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -4.5321 Å / Origin y: 28.4541 Å / Origin z: 6.798 Å
111213212223313233
T0.0526 Å20.0004 Å20.0129 Å2-0.0566 Å2-0.001 Å2--0.0571 Å2
L1.2102 °20.2036 °2-0.6338 °2-0.9189 °2-0.1792 °2--1.1805 °2
S-0.0723 Å °-0.0025 Å °-0.0992 Å °-0.056 Å °0.003 Å °-0.0548 Å °0.0467 Å °0.0167 Å °-0.0088 Å °
Refinement TLS groupSelection details: all

+
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