[English] 日本語
Yorodumi
- PDB-6tsp: Marasmius oreades agglutinin (MOA) inhibited by zinc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tsp
TitleMarasmius oreades agglutinin (MOA) inhibited by zinc
ComponentsAgglutinin
KeywordsSUGAR BINDING PROTEIN / fungal chimerolectin / papain-like cysteine protease / protease-substrate complex / calcium-binding protein / manganese-binding protein / toxin
Function / homologyAgglutinin, C-terminal / Agglutinin C-terminal / Ricin-type beta-trefoil lectin domain-like / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Papain-like cysteine peptidase superfamily / metal ion binding / Agglutinin
Function and homology information
Biological speciesMarasmius oreades (fairy-ring Marasmius)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsCordara, G. / Manna, D. / Krengel, U.
CitationJournal: Curr Res Struct Biol / Year: 2020
Title: Crystal structure of MOA in complex with a peptide fragment: a protease caught in flagranti
Authors: Manna, D. / Cordara, G. / Krengel, U.
History
DepositionDec 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,71019
Polymers32,3291
Non-polymers2,38218
Water2,468137
1
AAA: Agglutinin
hetero molecules

AAA: Agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,42038
Polymers64,6572
Non-polymers4,76336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_454-x+y-1,y,-z-1/21
Buried area11690 Å2
ΔGint-351 kcal/mol
Surface area23310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.071, 121.071, 99.624
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11AAA-519-

HOH

-
Components

-
Protein , 1 types, 1 molecules AAA

#1: Protein Agglutinin


Mass: 32328.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marasmius oreades (fairy-ring Marasmius)
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q8X123

-
Sugars , 2 types, 3 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpa1-3]DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1b_1-5][a1221m-1a_1-5][a2112h-1a_1-5]/1-2-3/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-Galp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpa1-3]DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2112h-1a_1-5][a1221m-1a_1-5]/1-2-1/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-Galp]{}}LINUCSPDB-CARE

-
Non-polymers , 6 types, 152 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M cacodylate/HCl pH 6.5, 16% PEG 8000, 0.5 M sodium acetate, 50 mM ZnCl2, 10 mM CaCl2, 12.5% DMSO, 5 mM DTT

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.28242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28242 Å / Relative weight: 1
ReflectionResolution: 1.85→46.4 Å / Num. obs: 64833 / % possible obs: 88.2 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.031 / Rrim(I) all: 0.073 / Net I/σ(I): 18.2
Reflection shellResolution: 1.85→1.88 Å / Rmerge(I) obs: 1.437 / Num. unique obs: 1507 / CC1/2: 0.489 / Rpim(I) all: 0.986 / Rrim(I) all: 1.767

-
Processing

Software
NameVersionClassification
REFMAC7.0.078refinement
XDSMar 15, 2019 BUILT=20190315data reduction
XDSMar 15, 2019 BUILT=20190315data scaling
PHASER7.0.078phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EF2

3ef2


Resolution: 1.85→46.4 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.923 / SU ML: 0.078 / Cross valid method: FREE R-VALUE / ESU R: 0.132 / ESU R Free: 0.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2347 1872 5.242 %
Rwork0.2068 --
all0.208 --
obs-35709 94.566 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.884 Å2
Baniso -1Baniso -2Baniso -3
1-1.483 Å20.742 Å20 Å2
2--1.483 Å20 Å2
3----4.811 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2278 0 132 137 2547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132559
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172184
X-RAY DIFFRACTIONr_angle_refined_deg0.8111.6893490
X-RAY DIFFRACTIONr_angle_other_deg0.5951.6285094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3775313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30523.84125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01415356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.43157
X-RAY DIFFRACTIONr_chiral_restr0.0110.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0410.022845
X-RAY DIFFRACTIONr_gen_planes_other0.0330.02548
X-RAY DIFFRACTIONr_nbd_refined0.2070.2477
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.21964
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21252
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1050.21075
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2124
X-RAY DIFFRACTIONr_metal_ion_refined0.1860.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.40.213
X-RAY DIFFRACTIONr_nbd_other0.2660.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.213
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1230.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2070.21
X-RAY DIFFRACTIONr_mcbond_it2.6753.3631207
X-RAY DIFFRACTIONr_mcbond_other2.6763.3631206
X-RAY DIFFRACTIONr_mcangle_it3.1065.0451517
X-RAY DIFFRACTIONr_mcangle_other3.1065.0451518
X-RAY DIFFRACTIONr_scbond_it3.3883.6741352
X-RAY DIFFRACTIONr_scbond_other3.3873.6741353
X-RAY DIFFRACTIONr_scangle_it4.4795.3971967
X-RAY DIFFRACTIONr_scangle_other4.4775.3971968
X-RAY DIFFRACTIONr_lrange_it5.19939.7692915
X-RAY DIFFRACTIONr_lrange_other5.19239.6852900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8890.511020.4371748X-RAY DIFFRACTION67.5923
1.889-1.9410.3691130.3781978X-RAY DIFFRACTION78.6386
1.941-1.9970.3831320.3172102X-RAY DIFFRACTION85.89
1.997-2.0590.3171220.2742227X-RAY DIFFRACTION92.8458
2.059-2.1260.281000.2542342X-RAY DIFFRACTION99.3895
2.126-2.2010.3131190.2612253X-RAY DIFFRACTION99.8737
2.201-2.2840.2551110.212194X-RAY DIFFRACTION100
2.284-2.3770.2691260.2282095X-RAY DIFFRACTION100
2.377-2.4830.2481250.2051996X-RAY DIFFRACTION100
2.483-2.6040.2221010.1721926X-RAY DIFFRACTION99.7539
2.604-2.7450.2151070.1611842X-RAY DIFFRACTION99.8975
2.745-2.9110.222980.1731749X-RAY DIFFRACTION99.9459
2.911-3.1120.2980.1781649X-RAY DIFFRACTION99.8857
3.112-3.3610.208800.1921547X-RAY DIFFRACTION99.9386
3.361-3.6810.207730.1971437X-RAY DIFFRACTION100
3.681-4.1150.2750.1861294X-RAY DIFFRACTION99.7813
4.115-4.750.16690.1441169X-RAY DIFFRACTION99.9193
4.75-5.8150.209510.1991006X-RAY DIFFRACTION99.8111
5.815-8.2110.266470.256791X-RAY DIFFRACTION100
8.211-46.40.319230.238493X-RAY DIFFRACTION98.4733

+
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