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- PDB-9udy: Crystal structure of recombinant mushroom Agaricus bisporus manno... -

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Basic information

Entry
Database: PDB / ID: 9udy
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 (common mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lectin-like fold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8422
Polymers18,7201
Non-polymers1221
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint2 kcal/mol
Surface area8390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.164, 43.982, 67.247
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lectin-like fold protein


Mass: 18719.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agaricus bisporus (common mushroom) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G1K3P4
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: sodium formate

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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: Mar 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→43.98 Å / Num. obs: 19365 / % possible obs: 100 % / Redundancy: 6.2 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.021 / Rrim(I) all: 0.052 / Χ2: 1.01 / Net I/σ(I): 21.3 / Num. measured all: 119287
Reflection shellResolution: 1.51→1.54 Å / % possible obs: 100 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.649 / Num. measured all: 3940 / Num. unique obs: 946 / CC1/2: 0.778 / Rpim(I) all: 0.356 / Rrim(I) all: 0.743 / Χ2: 0.87 / Net I/σ(I) obs: 2

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Processing

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

5eha


Resolution: 1.51→36.81 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.749 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19376 925 4.8 %RANDOM
Rwork0.13199 ---
obs0.13511 18393 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.837 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å2-0 Å2
2---0.27 Å20 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.51→36.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1204 0 8 90 1302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131240
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171092
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.6351689
X-RAY DIFFRACTIONr_angle_other_deg1.3531.582540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7255155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.79723.43367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81615189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.91157
X-RAY DIFFRACTIONr_chiral_restr0.0640.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021415
X-RAY DIFFRACTIONr_gen_planes_other00.02262
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_it5.7322.285624
X-RAY DIFFRACTIONr_mcbond_other5.6982.276622
X-RAY DIFFRACTIONr_mcangle_it6.8873.431777
X-RAY DIFFRACTIONr_mcangle_other6.8883.436778
X-RAY DIFFRACTIONr_scbond_it6.7132.667616
X-RAY DIFFRACTIONr_scbond_other6.7092.67617
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5593.84913
X-RAY DIFFRACTIONr_long_range_B_refined8.21827.9021352
X-RAY DIFFRACTIONr_long_range_B_other8.20527.7521340
X-RAY DIFFRACTIONr_rigid_bond_restr4.51232332
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.51→1.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 72 -
Rwork0.209 1337 -
obs--100 %

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