[English] 日本語
Yorodumi
- PDB-3zw0: Structure of BambL lectin from Burkholderia ambifaria -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zw0
TitleStructure of BambL lectin from Burkholderia ambifaria
Components(BAMBL LECTIN) x 2
KeywordsSUGAR BINDING PROTEIN / CYSTIC FIBROSIS / B-PROPELLER / HUMAN HISTO-BLOOD GROUP
Function / homologyLipocalin - #190 / Fucose-specific lectin / Fungal fucose-specific lectin / Lipocalin / Beta Barrel / Mainly Beta / alpha-L-fucopyranose / Fucose-binding lectin protein
Function and homology information
Biological speciesBURKHOLDERIA AMBIFARIA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAudfray, A. / Claudinon, J. / Abounit, S. / Ruvoen-Clouet, N. / Larson, G. / Wimmerova, M. / LePendu, J. / Romer, W. / Varrot, A. / Imberty, A.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Fucose-Binding Lectin from Opportunistic Pathogen Burkholderia Ambifaria Binds to Both Plant and Human Oligosaccharidic Epitopes.
Authors: Audfray, A. / Claudinon, J. / Abounit, S. / Ruvoen-Clouet, N. / Larson, G. / Smith, D.F. / Wimmerova, M. / Le Pendu, J. / Romer, W. / Varrot, A. / Imberty, A.
History
DepositionJul 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Other
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BAMBL LECTIN
B: BAMBL LECTIN
C: BAMBL LECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3424
Polymers28,1773
Non-polymers1641
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-16.8 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.110, 47.250, 98.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.2951, -0.9092, 0.2938), (0.08808, 0.2803, 0.9559), (-0.9514, 0.3079, -0.002639)-6.53, 15.05, -23.14
2given(-0.2979, 0.1261, -0.9462), (-0.9006, 0.2916, 0.3224), (0.3166, 0.9482, 0.0267)-25.05, -2.763, -12.01

-
Components

#1: Protein BAMBL LECTIN


Mass: 9387.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA AMBIFARIA (bacteria) / Strain: AMMD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0B4G1
#2: Protein BAMBL LECTIN


Mass: 9403.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA AMBIFARIA (bacteria) / Strain: AMMD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0B4G1
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.78 Å3/Da / Density % sol: 31.11 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9334
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.6→33.24 Å / Num. obs: 26647 / % possible obs: 93.7 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 26.6
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 13.4 / % possible all: 70.5

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BT9

2bt9


Resolution: 1.6→49.16 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.537 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.18842 1334 5 %RANDOM
Rwork0.14344 ---
obs0.14569 25224 93.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.177 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 11 399 2394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212112
X-RAY DIFFRACTIONr_bond_other_d0.0010.021322
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.882902
X-RAY DIFFRACTIONr_angle_other_deg0.84333180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8685272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78822.93592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60115273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6021513
X-RAY DIFFRACTIONr_chiral_restr0.0960.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02492
X-RAY DIFFRACTIONr_nbd_refined0.1550.2297
X-RAY DIFFRACTIONr_nbd_other0.230.21302
X-RAY DIFFRACTIONr_nbtor_refined0.1930.2948
X-RAY DIFFRACTIONr_nbtor_other0.1190.21051
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1690.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.242
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.921.51314
X-RAY DIFFRACTIONr_mcbond_other0.2761.5566
X-RAY DIFFRACTIONr_mcangle_it1.5422097
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1783798
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0654.5805
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 65 -
Rwork0.15 1293 -
obs--65.6 %

+
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