[English] 日本語
Yorodumi
- PDB-9udz: Crystal structure of recombinant mushroom Agaricus bisporus manno... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9udz
TitleCrystal structure of recombinant mushroom Agaricus bisporus mannose-binding protein with a longer C-terminal region
ComponentsLectin-like fold protein
KeywordsSUGAR BINDING PROTEIN / Lectin-like protein / Agaricus bisporus
Function / homologyLectin-like fold protein
Function and homology information
Biological speciesAgaricus bisporus (cultivated mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsYoshida, H. / Ismaya, W.T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Not funded Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Crystal structure of a recombinant Agaricus bisporus mushroom mannose-binding protein with a longer C-terminal region.
Authors: Yoshida, H. / Nakakita, S.I. / Rachmawati, H. / Tjandrawinata, R.R. / Ismaya, W.T.
History
DepositionApr 7, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lectin-like fold protein
B: Lectin-like fold protein


Theoretical massNumber of molelcules
Total (without water)37,4392
Polymers37,4392
Non-polymers00
Water41423
1
A: Lectin-like fold protein


Theoretical massNumber of molelcules
Total (without water)18,7201
Polymers18,7201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lectin-like fold protein


Theoretical massNumber of molelcules
Total (without water)18,7201
Polymers18,7201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.692, 44.121, 77.503
Angle α, β, γ (deg.)90.00, 128.34, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Lectin-like fold protein


Mass: 18719.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agaricus bisporus (cultivated mushroom)
Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G1K3P4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: sodium phosphate monohydrate, potassium phosphate dibasic

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.34→40.31 Å / Num. obs: 11521 / % possible obs: 98.8 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.054 / Rrim(I) all: 0.144 / Χ2: 1.03 / Net I/σ(I): 11.8
Reflection shellResolution: 2.34→2.42 Å / % possible obs: 97.7 % / Redundancy: 7 % / Rmerge(I) obs: 0.829 / Num. measured all: 7729 / Num. unique obs: 1106 / CC1/2: 0.744 / Rpim(I) all: 0.335 / Rrim(I) all: 0.895 / Χ2: 0.94 / Net I/σ(I) obs: 2.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EHA

5eha


Resolution: 2.34→40.31 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.634 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.449 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25872 569 4.9 %RANDOM
Rwork0.18724 ---
obs0.19088 10951 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.674 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.03 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.34→40.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2169 0 0 23 2192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132221
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171969
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.6373018
X-RAY DIFFRACTIONr_angle_other_deg1.2371.5824575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6585272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24323.388121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.60715343
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3611512
X-RAY DIFFRACTIONr_chiral_restr0.0580.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02478
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_it3.1613.7951106
X-RAY DIFFRACTIONr_mcbond_other3.1533.7951105
X-RAY DIFFRACTIONr_mcangle_it4.7975.661372
X-RAY DIFFRACTIONr_mcangle_other4.7975.6611373
X-RAY DIFFRACTIONr_scbond_it3.3544.0841115
X-RAY DIFFRACTIONr_scbond_other3.3534.0841116
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0715.9751647
X-RAY DIFFRACTIONr_long_range_B_refined7.10341.6442340
X-RAY DIFFRACTIONr_long_range_B_other7.10241.6562341
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.34→2.401 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 37 -
Rwork0.244 789 -
obs--97.98 %

+
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