[English] 日本語
Yorodumi
- PDB-4p9x: Structure of ConA/Rh3Glu complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4p9x
TitleStructure of ConA/Rh3Glu complex
ComponentsConcanavalin-A
KeywordsSUGAR BINDING PROTEIN / lectin / carbohydrate / porous protein framework
Function / homology
Function and homology information


regulation of defense response to virus / D-mannose binding / defense response / 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, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Chem-R3G / Concanavalin-A
Similarity search - Component
Biological speciesCanavalia ensiformis (jack bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.06 Å
AuthorsSakai, F. / Weiss, M.S. / Chen, G.
CitationJournal: To Be Published
Title: Structure of ConA/Rh3Glu complex
Authors: Sakai, F. / Weiss, F.S. / Chen, G.
History
DepositionApr 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_nat ...citation / entity_src_nat / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Concanavalin-A
B: Concanavalin-A
C: Concanavalin-A
D: Concanavalin-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,14916
Polymers102,4904
Non-polymers3,66012
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9690 Å2
ΔGint-112 kcal/mol
Surface area34110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.173, 116.028, 84.255
Angle α, β, γ (deg.)90.000, 95.980, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Concanavalin-A / Con A


Mass: 25622.385 Da / Num. of mol.: 4 / Fragment: UNP residues 164-281, 30-148
Source method: isolated from a genetically manipulated source
Source: (natural) Canavalia ensiformis (jack bean) / References: UniProt: P02866
#2: Chemical
ChemComp-R3G / 2-[2-(2-{4-[(alpha-D-glucopyranosyloxy)methyl]-1H-1,2,3-triazol-1-yl}ethoxy)ethoxy]ethyl 2-[3,6-bis(diethylamino)-9H-xanthen-9-yl]benzoate


Mass: 819.940 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C43H57N5O11
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.99 Å3/Da / Density % sol: 69.19 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 7.2
Details: buffer: 20 mM HEPES, 5 mM of CaCl2, and 5 mM of MnCl2; pH = 7.2. The crystal was obtained by diffusion method in glass tube sequentially put with ConA solution, pure buffer, and the ligand solution.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.06→39.4 Å / Num. obs: 98988 / % possible obs: 99.7 % / Redundancy: 3.42 % / Net I/σ(I): 17.63

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
MOLREP11.0.02phasing
PDB_EXTRACT3.14data extraction
REFMAC5.6.0117refinement
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→30 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.855 / WRfactor Rfree: 0.2845 / WRfactor Rwork: 0.2369 / FOM work R set: 0.8099 / SU B: 10.555 / SU ML: 0.138 / SU R Cruickshank DPI: 0.1736 / SU Rfree: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2953 2981 3 %RANDOM
Rwork0.245 96007 --
obs0.2465 96007 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 66.18 Å2 / Biso mean: 21.557 Å2 / Biso min: 8.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20.42 Å2
2--1.37 Å20 Å2
3----0.8 Å2
Refinement stepCycle: final / Resolution: 2.06→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7236 0 244 114 7594
Biso mean--16.25 28.61 -
Num. residues----948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.027660
X-RAY DIFFRACTIONr_angle_refined_deg2.1111.97710448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5055944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08724.872312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.418151156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0311524
X-RAY DIFFRACTIONr_chiral_restr0.1440.21184
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215784
LS refinement shellResolution: 2.06→2.113 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 221 -
Rwork0.288 6929 -
all-7150 -
obs--99.6 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.56940.12750.08581.81760.0061.3626-0.00410.0026-0.05650.03120.002-0.07360.01610.03470.00210.02550.0076-0.02050.0031-0.00860.060914.643-0.23125.247
22.5847-0.08220.25871.57670.2941.14010.03120.0543-0.041-0.0294-0.02740.1128-0.0411-0.1023-0.00380.06290.0247-0.02060.06470.02310.0932-21.357-2.40818.706
31.47310.3319-0.13841.7807-0.38612.00990.0170.029-0.0212-0.0092-0.0106-0.0458-0.05110.0136-0.00640.09050.0101-0.0140.00380.00310.04030.195-31.46238.414
41.0781-0.28890.01371.56860.22712.4854-0.01520.0607-0.069-0.0371-0.02660.0274-0.0594-0.00730.04180.1103-0.0257-0.00910.0506-0.03580.0677-2.504-29.5172.025
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 237
2X-RAY DIFFRACTION1A301 - 303
3X-RAY DIFFRACTION1A403 - 406
4X-RAY DIFFRACTION2B1 - 237
5X-RAY DIFFRACTION2B301 - 303
6X-RAY DIFFRACTION2B404 - 407
7X-RAY DIFFRACTION3C1 - 237
8X-RAY DIFFRACTION3C301 - 303
9X-RAY DIFFRACTION3C405 - 408
10X-RAY DIFFRACTION4D1 - 237
11X-RAY DIFFRACTION4D301 - 303
12X-RAY DIFFRACTION4D401 - 403

+
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://pdbjlvh1.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