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- PDB-9lxl: Crystal structure of GH29 family alpha-L-fucosidase from Fusarium... -

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Basic information

Entry
Database: PDB / ID: 9lxl
TitleCrystal structure of GH29 family alpha-L-fucosidase from Fusarium proliferatum LE1
Componentsalpha-L-fucosidase
KeywordsHYDROLASE / alpha-L-fucosidase / GH29 / Fusarium Proliferatum
Function / homology
Function and homology information


alpha-L-fucosidase / alpha-L-fucosidase activity / fucose metabolic process / glycoside catabolic process
Similarity search - Function
Alpha-L-fucosidase, C-terminal / Alpha-L-fucosidase C-terminal domain / Alpha-L-fucosidase, metazoa-type / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / AZIDE ION / alpha-L-fucosidase
Similarity search - Component
Biological speciesGibberella intermedia (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.191 Å
AuthorsKorban, S.A. / Borshchevskiy, V.I. / Pospelov, V.A. / Bobrov, K.S. / Ivanova, D.N. / Kulminskaya, A.A.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation1023031500033-1-1.6.7;1.6.4;1.6.8 Russian Federation
CitationJournal: To Be Published
Title: Crystal structure of GH29 family alpha-L-fucosidase from Fusarium proliferatum LE1
Authors: Korban, S.A. / Borshchevskiy, V.I. / Pospelov, V.A. / Bobrov, K.S. / Ivanova, D.N. / Kulminskaya, A.A.
History
DepositionFeb 18, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alpha-L-fucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,47115
Polymers69,0981
Non-polymers1,37314
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint1 kcal/mol
Surface area21810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.757, 76.757, 225.338
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Protein / Sugars , 2 types, 4 molecules A

#1: Protein alpha-L-fucosidase / Alpha-L-fucosidase GH29


Mass: 69097.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gibberella intermedia (fungus) / Gene: FPRO05_08134 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A365NIL9, alpha-L-fucosidase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 245 molecules

#3: 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
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: N3
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 0.1M Bis-Tris pH 6.7, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17UM / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Dec 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.191→72.657 Å / Num. obs: 24244 / % possible obs: 91.7 % / Redundancy: 14.6 % / Biso Wilson estimate: 37.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.058 / Net I/σ(I): 9.3
Reflection shellResolution: 2.191→2.441 Å / Num. unique obs: 1212 / CC1/2: 0.589

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Processing

Software
NameVersionClassification
autoPROCautoPROC 1.0.5data processing
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.191→63.44 Å / SU ML: 0.2481 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.9997
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2339 1233 5.09 %
Rwork0.202 23008 -
obs0.2036 24241 67.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.81 Å2
Refinement stepCycle: LAST / Resolution: 2.191→63.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4479 0 90 234 4803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01014724
X-RAY DIFFRACTIONf_angle_d1.48046435
X-RAY DIFFRACTIONf_chiral_restr0.0902685
X-RAY DIFFRACTIONf_plane_restr0.0123836
X-RAY DIFFRACTIONf_dihedral_angle_d11.72781653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.191-2.280.277530.3347139X-RAY DIFFRACTION3.71
2.28-2.380.3638410.3126527X-RAY DIFFRACTION14.63
2.38-2.510.3518640.30521265X-RAY DIFFRACTION34.38
2.51-2.670.3081320.28832378X-RAY DIFFRACTION64.15
2.67-2.870.27451800.28023330X-RAY DIFFRACTION89.56
2.87-3.160.30352000.2443719X-RAY DIFFRACTION99.67
3.16-3.620.24141910.20713786X-RAY DIFFRACTION100
3.62-4.560.1982070.15613818X-RAY DIFFRACTION100
4.56-63.440.19192150.17274046X-RAY DIFFRACTION99.95
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)
10.303565097811-0.0502252102533-0.04508665016760.5879716349070.08528284475640.556089816641-0.0251893178317-0.07067103932270.0239523477410.1952013117580.00214200146611-0.1712073779450.1114539420720.094472755188-0.1877309171880.826801663292-0.0386336192122-0.391097653090.2073041601970.01309467120450.356163272029-24.838040483130.192576418830.4498119878
20.895222633486-0.309598433741-0.4428308177520.793001874190.921270415082.59465492722-0.133879496827-0.07126936647690.002177807550150.53882868866-0.02788482232760.1467089575370.156465730278-0.2619275373830.2115417969540.996741231388-0.0980180356504-0.2232518826910.252663357836-0.01482141088670.415631008397-39.424503988929.574421836234.8420817646
30.013794723459-0.02831156603950.05199529963560.2040709555840.07328860354170.2896847863810.00440731899124-0.05268385230350.02200838880680.238891800166-0.0370097655633-0.0810515405930.0533194203415-0.0199316988261-0.07401279983491.02784987058-0.0940594165769-0.4105883071560.226436947291-0.009320481118240.371080596734-27.250667898324.480353362239.2705215231
40.100982127218-0.110498266044-0.03544445483370.22325368088-0.02847294743480.0763942635388-0.00505074605708-0.028131383510.03217325369620.06860270712770.0307067864011-0.0826505881619-0.02008024108510.0161350191750.09614973696450.921293178604-0.040329046362-0.4098975534680.1426874675080.003577341642010.480837702359-14.543959821524.442987015531.0245404456
50.415943986444-0.2733517662460.1473371978230.334895538487-0.1943638177640.2508902882290.006831565493660.07738465287910.1337875034590.0844212014227-0.0598385818751-0.0943481050440.03419127331280.03047804628360.02075184272670.5439932984150.00202115524309-0.3467407168610.1261041938690.1030273642020.252971431662-26.206560894432.638689086212.0105939907
63.07550155928-1.24848368206-0.2977101925741.53395210071-0.2140429974041.593784862980.2484842540670.8201195330260.115725593026-0.42896656133-0.255996121993-0.2736205122330.5934639080380.2179764418270.00762324053290.6732119549120.145605991445-0.1679687192560.5406152940690.08428114542770.331333433968-20.951714344327.9249696342-10.3121398588
71.696530287730.820391619698-0.8554185410511.064122427850.5125817255782.86100531080.1526520084250.5454164754050.0746206076674-0.0748045109621-0.229800281828-0.2928773857820.237074391170.0460983928370.07257367957520.6484318347850.0107944215435-0.2127221420580.4401405069910.1423423696340.338242940155-20.889663514127.9782761558-6.54647814886
86.708810834441.08565788997-0.9957560905671.87535859177-2.808508489587.84939075375-0.136067487372-0.31825205879-0.8299028780710.300893488692-0.0962741888087-1.39894366961.181110757541.661927838840.2426575351820.6705558863070.275813588606-0.2232467233550.717310439534-0.0176512019360.957519309794-0.5919385901224.65245516143.07379570206
94.6179859524-1.104481103020.4908809735754.786015683140.499495589362.312195367060.11982927997-0.504674710081-0.1537994535060.591789780492-0.0732055600891-1.376077403270.2447182929241.46636884247-0.04823576008260.6386889324860.117123251709-0.2237679982721.56359181030.1453120168821.107873837136.8617040850331.26868183183.37233802414
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 67 )3 - 671 - 65
22chain 'A' and (resid 68 through 133 )68 - 13366 - 131
33chain 'A' and (resid 134 through 219 )134 - 219132 - 217
44chain 'A' and (resid 220 through 284 )220 - 284218 - 282
55chain 'A' and (resid 285 through 410 )285 - 410283 - 408
66chain 'A' and (resid 411 through 475 )411 - 475409 - 473
77chain 'A' and (resid 476 through 504 )476 - 504474 - 502
88chain 'A' and (resid 505 through 541 )505 - 541503 - 539
99chain 'A' and (resid 542 through 585 )542 - 585540 - 583

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