[English] 日本語
Yorodumi
- PDB-4zlb: Structural studies on a non-toxic homologue of type II RIPs from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zlb
TitleStructural studies on a non-toxic homologue of type II RIPs from Momordica charantia (bitter gourd) in complex with lactose
Components(rRNA N-glycosidase) x 2
KeywordsHYDROLASE / beta-trefoil / Type II RIPs / Galactose binding lectin
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / 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 type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily ...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 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
beta-lactose / beta-D-xylopyranose / Ribosome-inactivating protein
Similarity search - Component
Biological speciesMomordica charantia (bitter melon)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsChandran, T. / Sharma, A. / Vijayan, M.
Funding support India, 1items
OrganizationGrant numberCountry
DST, SERB India
Citation
Journal: J.Biosci. / Year: 2015
Title: Structural studies on a non-toxic homologue of type II RIPs from bitter gourd: Molecular basis of non-toxicity, conformational selection and glycan structure.
Authors: Chandran, T. / Sharma, A. / Vijayan, M.
#1: Journal: Acta Crystallogr. F Biol. Crystallogr. / Year: 2010
Title: Crystallization and preliminary X-ray studies of a galactose-specific lectin from the seeds of bitter gourd (Momordica charantia).
Authors: Sharma, A. / Pohlentz, G. / Bobbili, K.B. / Jeyaprakash, A.A. / Chandran, T. / Mormann, M. / Swamy, M.J. / Vijayan, M.
#2: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013
Title: The sequence and structure of snake gourd (Trichosanthes anguina) seed lectin, a three-chain nontoxic homologue of type II RIPs.
Authors: Sharma, A. / Pohlentz, G. / Bobbili, K.B. / Jeyaprakash, A.A. / Chandran, T. / Mormann, M. / Swamy, M.J. / Vijayan, M.
History
DepositionMay 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: rRNA N-glycosidase
B: rRNA N-glycosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5488
Polymers56,6602
Non-polymers1,8896
Water3,225179
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-0 kcal/mol
Surface area22060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.380, 139.570, 45.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein rRNA N-glycosidase


Mass: 27642.234 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 24-270 / Source method: isolated from a natural source / Source: (natural) Momordica charantia (bitter melon) / References: UniProt: B7X8M2, rRNA N-glycosylase
#2: Protein rRNA N-glycosidase


Mass: 29017.416 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 287-547 / Source method: isolated from a natural source / Source: (natural) Momordica charantia (bitter melon) / References: UniProt: B7X8M2, rRNA N-glycosylase

-
Sugars , 6 types, 6 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#7: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#8: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 1 types, 179 molecules

#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 0.1M HEPES, 25% w/v PEG 10000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 7, 2012
RadiationMonochromator: Mirrors POLAR 0.000 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.55→69.79 Å / Num. obs: 26759 / % possible obs: 97.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 7
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2 / % possible all: 93.3

-
Processing

SoftwareName: REFMAC / Version: 5.8.0107 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z8S

4z8s


Resolution: 2.55→69.79 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.841 / SU B: 16.327 / SU ML: 0.317 / Cross valid method: THROUGHOUT / ESU R: 0.463 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1340 5 %RANDOM
Rwork0.246 ---
obs0.248 25385 97.1 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.36 Å2
Baniso -1Baniso -2Baniso -3
1-5.18 Å20 Å20 Å2
2---3.49 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 2.55→69.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3970 0 123 179 4272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.024185
X-RAY DIFFRACTIONr_bond_other_d0.0010.023836
X-RAY DIFFRACTIONr_angle_refined_deg1.151.9715700
X-RAY DIFFRACTIONr_angle_other_deg0.94838826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3395506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42624.974191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11315666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0961519
X-RAY DIFFRACTIONr_chiral_restr0.1020.2670
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024719
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02969
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.613.142030
X-RAY DIFFRACTIONr_mcbond_other0.613.142029
X-RAY DIFFRACTIONr_mcangle_it1.124.7082534
X-RAY DIFFRACTIONr_mcangle_other1.1194.7082535
X-RAY DIFFRACTIONr_scbond_it0.5363.3022154
X-RAY DIFFRACTIONr_scbond_other0.5363.3022154
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9454.9273167
X-RAY DIFFRACTIONr_long_range_B_refined2.79225.1594744
X-RAY DIFFRACTIONr_long_range_B_other2.79225.1624745
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 70 -
Rwork0.423 1759 -
obs--91.86 %

+
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