[English] 日本語
Yorodumi
- PDB-2q3n: Agglutinin from Abrus Precatorius (APA-I) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q3n
TitleAgglutinin from Abrus Precatorius (APA-I)
Components
  • Agglutinin-1 A chain
  • Agglutinin-1 B chain
KeywordsPLANT PROTEIN / RIBOSOME-INACTIVATING PROTEIN / IMMUNOTOXIN / AGGLUTININ ABRIN
Function / homology
Function and homology information


positive regulation of apoptotic process in another organism / rRNA N-glycosylase / rRNA N-glycosylase activity / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / defense response / toxin activity / carbohydrate binding / negative regulation of translation
Similarity search - Function
Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesAbrus precatorius (Indian licorice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBagaria, A. / Surendranath, K. / Ramagopal, U.A. / Ramakumar, S. / Karande, A.A.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure-Function Analysis and Insights into the Reduced Toxicity of Abrus precatorius Agglutinin I in Relation to Abrin.
Authors: Bagaria, A. / Surendranath, K. / Ramagopal, U.A. / Ramakumar, S. / Karande, A.A.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
SupersessionJun 26, 2007ID: 2AMZ
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 30, 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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). Author stated the biological unit of the protein is a non-obligate tetramer.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Agglutinin-1 A chain
B: Agglutinin-1 B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5795
Polymers58,9152
Non-polymers6643
Water0
1
A: Agglutinin-1 A chain
B: Agglutinin-1 B chain
hetero molecules

A: Agglutinin-1 A chain
B: Agglutinin-1 B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,15810
Polymers117,8314
Non-polymers1,3276
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-15 kcal/mol
Surface area21350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.122, 141.122, 105.253
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by a two fold rotation.

-
Components

#1: Protein Agglutinin-1 A chain


Mass: 28908.645 Da / Num. of mol.: 1 / Fragment: residues 21-280 / Source method: isolated from a natural source / Source: (natural) Abrus precatorius (Indian licorice) / References: UniProt: Q9M6E9, rRNA N-glycosylase
#2: Protein Agglutinin-1 B chain


Mass: 30006.816 Da / Num. of mol.: 1 / Fragment: residues 281-547 / Source method: isolated from a natural source / Source: (natural) Abrus precatorius (Indian licorice) / References: UniProt: Q9M6E9
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.45 Å3/Da / Density % sol: 72.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, TRIS-HCL BUFFER, PH 8.5, , VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.978 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 2005
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.5→29.31 Å / Num. obs: 11360 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.1
Reflection shellResolution: 3.5→3.7 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.3 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Abrin-a (PDB code: 1ABR)
Resolution: 3.5→29.31 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.849 / SU B: 47.287 / SU ML: 0.35 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.58 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25547 1115 9.8 %RANDOM
Rwork0.19481 ---
obs0.20079 10246 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 51.741 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3983 0 45 0 4028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224125
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.9525621
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4715506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.28524.27185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.52715664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1251524
X-RAY DIFFRACTIONr_chiral_restr0.1270.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023121
X-RAY DIFFRACTIONr_nbd_refined0.2660.22007
X-RAY DIFFRACTIONr_nbtor_refined0.3260.22765
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2162
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2760.24
X-RAY DIFFRACTIONr_mcbond_it0.2821.52565
X-RAY DIFFRACTIONr_mcangle_it0.52324100
X-RAY DIFFRACTIONr_scbond_it0.79831782
X-RAY DIFFRACTIONr_scangle_it1.3874.51521
LS refinement shellResolution: 3.501→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 62 -
Rwork0.251 518 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.297-1.86410.62214.77331.27095.69210.18620.4475-0.0442-0.7555-0.23010.1431-0.0673-0.12040.0439-0.2275-0.0644-0.0062-0.3853-0.0158-0.133238.161660.134642.5006
26.2657-4.585-1.82066.35782.42765.2385-0.0793-0.2464-0.10880.1947-0.01480.41930.3774-0.35550.0941-0.3107-0.1936-0.0357-0.3564-0.1356-0.073231.866465.145761.3771
38.0848-2.3184-1.9678.24641.57384.9759-0.1498-0.2951-0.49630.52960.1030.70240.2374-0.1760.0467-0.3367-0.07390.1747-0.084-0.12870.039918.062379.883380.4323
48.5145-0.8131-2.48395.61310.29044.6492-0.0751-0.82820.34720.52140.4435-0.5965-0.15011.0232-0.3684-0.2807-0.115-0.0753-0.0579-0.3154-0.056445.259975.365273.231
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1663 - 166
2X-RAY DIFFRACTION2AA167 - 248167 - 248
3X-RAY DIFFRACTION3BB7 - 1437 - 143
4X-RAY DIFFRACTION4BB144 - 267144 - 267

+
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