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- PDB-21ap: Magnaporthe oryzae GH43F -

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Basic information

Entry
Database: PDB / ID: 21ap
TitleMagnaporthe oryzae GH43F
ComponentsBeta-xylosidase C-terminal Concanavalin A-like domain-containing protein
KeywordsHYDROLASE / Complex
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
: / Beta-xylosidase, C-terminal Concanavalin A-like domain / Beta xylosidase C-terminal Concanavalin A-like domain / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Beta-xylosidase C-terminal Concanavalin A-like domain-containing protein
Similarity search - Component
Biological speciesPyricularia oryzae (rice blast fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChen, Y.H. / Zhang, C.R. / Wen, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Magnaporthe oryzae GH43F
Authors: Chen, Y.H. / Zhang, C.R. / Wen, Z.
History
DepositionDec 5, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-xylosidase C-terminal Concanavalin A-like domain-containing protein
B: Beta-xylosidase C-terminal Concanavalin A-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,5764
Polymers122,3322
Non-polymers2442
Water16,916939
1
A: Beta-xylosidase C-terminal Concanavalin A-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2882
Polymers61,1661
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-xylosidase C-terminal Concanavalin A-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2882
Polymers61,1661
Non-polymers1221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.030, 80.030, 379.702
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Beta-xylosidase C-terminal Concanavalin A-like domain-containing protein


Mass: 61166.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia oryzae (rice blast fungus) / Gene: PoMZ_10733 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4P7MY98
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 100 mM Tris pH 8.5, 200 mM MgCl2, 20%(w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97854 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 2.1→78.31 Å / Num. obs: 73577 / % possible obs: 99.9 % / Redundancy: 10.6 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02683 / Rpim(I) all: 0.02683 / Rrim(I) all: 0.03794 / Rsym value: 0.03794 / Net I/σ(I): 16.58
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 7211 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIXv1.20.1refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→78.31 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2152 3636 4.94 %
Rwork0.1781 --
obs0.1799 73549 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→78.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8531 0 16 939 9486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048805
X-RAY DIFFRACTIONf_angle_d0.67312038
X-RAY DIFFRACTIONf_dihedral_angle_d13.0693137
X-RAY DIFFRACTIONf_chiral_restr0.0491270
X-RAY DIFFRACTIONf_plane_restr0.0051593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.25671450.23372626X-RAY DIFFRACTION100
2.13-2.160.28191410.24222646X-RAY DIFFRACTION100
2.16-2.190.29981330.24362616X-RAY DIFFRACTION100
2.19-2.220.30091370.22512683X-RAY DIFFRACTION100
2.22-2.250.25821590.22742558X-RAY DIFFRACTION100
2.25-2.290.24311350.19662692X-RAY DIFFRACTION100
2.29-2.330.21851170.19952614X-RAY DIFFRACTION100
2.33-2.370.24921360.1982655X-RAY DIFFRACTION100
2.37-2.420.22841600.19662647X-RAY DIFFRACTION100
2.42-2.470.2651220.20112651X-RAY DIFFRACTION100
2.47-2.520.27141300.20262681X-RAY DIFFRACTION100
2.52-2.580.25781510.19922668X-RAY DIFFRACTION100
2.58-2.650.24461230.19052629X-RAY DIFFRACTION100
2.65-2.720.22961450.20162668X-RAY DIFFRACTION100
2.72-2.80.25861420.19392662X-RAY DIFFRACTION100
2.8-2.890.22911290.19892695X-RAY DIFFRACTION100
2.89-2.990.21221490.19282659X-RAY DIFFRACTION100
2.99-3.110.24811390.18322674X-RAY DIFFRACTION100
3.11-3.250.22371370.17692702X-RAY DIFFRACTION100
3.25-3.420.21071410.16872699X-RAY DIFFRACTION100
3.42-3.640.20941350.16332744X-RAY DIFFRACTION100
3.64-3.920.15351330.15422706X-RAY DIFFRACTION100
3.92-4.310.18581320.14632764X-RAY DIFFRACTION100
4.31-4.940.15871680.13672748X-RAY DIFFRACTION100
4.94-6.220.21131320.16662835X-RAY DIFFRACTION100
6.22-100.21591650.18842991X-RAY DIFFRACTION99

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