[English] 日本語
Yorodumi
- PDB-1fnz: A bark lectin from robinia pseudoacacia in complex with N-acetylg... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fnz
TitleA bark lectin from robinia pseudoacacia in complex with N-acetylgalactosamine
ComponentsBARK AGGLUTININ I, POLYPEPTIDE A
KeywordsSUGAR BINDING PROTEIN / jelly roll
Function / homology
Function and homology information


carbohydrate binding / metal ion binding
Similarity search - Function
Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / : / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / Bark agglutinin I polypeptide A
Similarity search - Component
Biological speciesRobinia pseudoacacia (black locust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.05 Å
AuthorsRabijns, A. / Verboven, C. / Rouge, P. / Barre, A. / Van Damme, E.J. / Peumans, W.J. / De Ranter, C.J.
Citation
Journal: Proteins / Year: 2001
Title: Structure of a legume lectin from the bark of Robinia pseudoacacia and its complex with N-acetylgalactosamine
Authors: Rabijns, A. / Verboven, C. / Rouge, P. / Barre, A. / Van Damme, E.J. / Peumans, W.J. / De Ranter, C.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: A legume lectin from the bark of Robinia pseudoacacia crystallizes in two crystal forms: preliminary diffraction analyses
Authors: Rabijns, A. / Verboven, C. / Van Damme, E.J. / Peumans, W.J. / De Ranter, C.J.
History
DepositionAug 24, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 24, 2001Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BARK AGGLUTININ I, POLYPEPTIDE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8723
Polymers25,6111
Non-polymers2612
Water2,702150
1
A: BARK AGGLUTININ I, POLYPEPTIDE A
hetero molecules

A: BARK AGGLUTININ I, POLYPEPTIDE A
hetero molecules

A: BARK AGGLUTININ I, POLYPEPTIDE A
hetero molecules

A: BARK AGGLUTININ I, POLYPEPTIDE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,48812
Polymers102,4424
Non-polymers1,0458
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_756-x+2,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area8360 Å2
ΔGint-73 kcal/mol
Surface area33690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.622, 76.231, 118.243
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein BARK AGGLUTININ I, POLYPEPTIDE A / BARK LECTIN


Mass: 25610.604 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-268 / Source method: isolated from a natural source / Source: (natural) Robinia pseudoacacia (black locust) / Tissue: BARK / References: UniProt: Q41159
#2: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAMINO ACID HETEROGENEITY IS PRESENT FOR THIS PROTEIN. AMINO ACIDS DIFFER DEPENDING ON THE PLANT SOURCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.2M ammonium sulphate, 30% polyethylene glycol 4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 8
Details: Rabijns, A., (2000) Acta Crystallogr., Sect.D, 56, 1638.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mg/mlprotein1drop
20.1 MTris1drop
30.2 Mammonium sulfate1reservoir
430 %(w/v)PEG40001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 22, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 18204 / Num. obs: 18204 / % possible obs: 77.2 % / Observed criterion σ(F): 1.41 / Observed criterion σ(I): 2 / Redundancy: 2.94 % / Biso Wilson estimate: 21.748 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.87
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.95 % / Rmerge(I) obs: 0.278 / Num. unique all: 893 / % possible all: 96.5
Reflection
*PLUS
Lowest resolution: 20 Å / Observed criterion σ(I): 2 / Num. measured all: 53508

-
Processing

Software
NameClassification
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.05→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1788 9.822 %RANDOM
Rwork0.197 ---
all0.199 18204 --
obs0.199 14502 96.9 %-
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1792 0 16 150 1958
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.392
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_torsion_deg25.936
X-RAY DIFFRACTIONc_torsion_impr_deg0.808
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.197
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