[English] 日本語
Yorodumi
- PDB-1tp8: CRYSTAL STRUCTURE OF A GALACTOSE SPECIFIC LECTIN FROM ARTOCARPUS ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tp8
TitleCRYSTAL STRUCTURE OF A GALACTOSE SPECIFIC LECTIN FROM ARTOCARPUS HIRSUTA IN COMPLEX WITH METHYL-a-D-GALACTOSE
Components
  • AGGLUTININ ALPHA CHAIN
  • AGGLUTININ BETA CHAIN
KeywordsSUGAR BINDING PROTEIN / Artocarpus hirsuta / Moraceae plant lectins / Jacalin family / Post-translational modification / Carbohydrate specificity / Methyl--D-galactose / Three-dimensional structure / -prism I fold
Function / homology
Function and homology information


IgA binding / carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
methyl alpha-D-galactopyranoside / Agglutinin alpha chain / Agglutinin beta-3 chain
Similarity search - Component
Biological speciesArtocarpus hirsutus (aini)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRao, K.N. / Suresh, C.G. / Katre, U.V. / Gaikwad, S.M. / Khan, M.I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Two orthorhombic crystal structures of a galactose-specific lectin from Artocarpus hirsuta in complex with methyl-alpha-D-galactose.
Authors: Rao, K.N. / Suresh, C.G. / Katre, U.V. / Gaikwad, S.M. / Khan, M.I.
History
DepositionJun 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 525SOLVENT MOLECULES SOLVENT MOLECULES 1 - 31 ARE ASSOCIATED WITH COMPLEX A-B. SOLVENT MOLECULES 101- ...SOLVENT MOLECULES SOLVENT MOLECULES 1 - 31 ARE ASSOCIATED WITH COMPLEX A-B. SOLVENT MOLECULES 101-130 ARE ASSOCIATED WITH COMPLEX A-B. SOLVENT MOLECULES 201-227 ARE ASSOCIATED WITH COMPLEX A-B. SOLVENT MOLECULES 301-329 ARE ASSOCIATED WITH COMPLEX A-B.
Remark 999SEQUENCE sEQUENCE OF THESE MOLECULES IS NOT YET AVAILABLE IN ANY SEQUENCE DATABASE

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AGGLUTININ ALPHA CHAIN
B: AGGLUTININ BETA CHAIN
C: AGGLUTININ ALPHA CHAIN
D: AGGLUTININ BETA CHAIN
E: AGGLUTININ ALPHA CHAIN
F: AGGLUTININ BETA CHAIN
G: AGGLUTININ ALPHA CHAIN
H: AGGLUTININ BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,44312
Polymers66,6668
Non-polymers7774
Water1,24369
1
A: AGGLUTININ ALPHA CHAIN
B: AGGLUTININ BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8613
Polymers16,6672
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-10 kcal/mol
Surface area8030 Å2
MethodPISA
2
C: AGGLUTININ ALPHA CHAIN
D: AGGLUTININ BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8613
Polymers16,6672
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-8 kcal/mol
Surface area8570 Å2
MethodPISA
3
E: AGGLUTININ ALPHA CHAIN
F: AGGLUTININ BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8613
Polymers16,6672
Non-polymers1941
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-10 kcal/mol
Surface area8020 Å2
MethodPISA
4
G: AGGLUTININ ALPHA CHAIN
H: AGGLUTININ BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8613
Polymers16,6672
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-9 kcal/mol
Surface area8570 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12220 Å2
ΔGint-73 kcal/mol
Surface area25380 Å2
MethodPISA
6
E: AGGLUTININ ALPHA CHAIN
F: AGGLUTININ BETA CHAIN
G: AGGLUTININ ALPHA CHAIN
H: AGGLUTININ BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7216
Polymers33,3334
Non-polymers3882
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-29 kcal/mol
Surface area14440 Å2
MethodPISA
7
A: AGGLUTININ ALPHA CHAIN
B: AGGLUTININ BETA CHAIN
C: AGGLUTININ ALPHA CHAIN
D: AGGLUTININ BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7216
Polymers33,3334
Non-polymers3882
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-28 kcal/mol
Surface area14490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.900, 121.900, 131.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
AGGLUTININ ALPHA CHAIN


Mass: 14605.298 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: SEEDS / Source: (natural) Artocarpus hirsutus (aini) / References: UniProt: P18670*PLUS
#2: Protein/peptide
AGGLUTININ BETA CHAIN


Mass: 2061.253 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Chemically Synthesized / References: UniProt: P18673*PLUS
#3: Sugar
ChemComp-AMG / methyl alpha-D-galactopyranoside / ALPHA-METHYL-D-GALACTOSIDE / methyl alpha-D-galactoside / methyl D-galactoside / methyl galactoside / Methyl-α-D-galactose


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H14O6
IdentifierTypeProgram
DGalp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-methyl-galactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 6 Å3/Da / Density % sol: 79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M PO4 BUFFER, 35-40% AMMONIUM SULPHATE,METHYL ALPHA GALACTOSE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: CONFOCAL
RadiationMonochromator: MIRROR OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→29.73 Å / Num. all: 28782 / Num. obs: 28782 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.55 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 19.3
Reflection shellResolution: 3→3.5 Å / Redundancy: 4 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 7.22 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
MAR345data collection
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JAC

1jac


Resolution: 3→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: FREE R FACTOR / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2374 1316 RANDOM
Rwork0.19309 --
all-37497 -
obs-26013 -
Displacement parametersBiso mean: 36.53 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4584 0 52 69 4705
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg2.2
X-RAY DIFFRACTIONr_bond_refined_d0.008
LS refinement shellResolution: 3→3.29 Å
RfactorNum. reflection% reflection
Rfree0.263 258 -
Rwork0.203 --
obs-5089 75 %

+
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