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- PDB-4ni3: Crystal Structure of GH29 family alpha-L-fucosidase from Fusarium... -

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Basic information

Entry
Database: PDB / ID: 4ni3
TitleCrystal Structure of GH29 family alpha-L-fucosidase from Fusarium graminearum in the closed form
ComponentsAlpha-fucosidase GH29
KeywordsHYDROLASE / fucosidase / GH29 / glycoside hydrolase / TIM barrel / crystallin
Function / homology
Function and homology information


alpha-L-fucosidase / alpha-L-fucosidase activity / fucose metabolic 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 / Crystallins / Gamma-B Crystallin; domain 1 / Gamma-crystallin-like / Golgi alpha-mannosidase II ...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 / Crystallins / Gamma-B Crystallin; domain 1 / Gamma-crystallin-like / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesFusarium graminearum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3993 Å
AuthorsCao, H. / Walton, J.D. / Brumm, P. / Phillips Jr., G.N.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structure and Substrate Specificity of a Eukaryotic Fucosidase from Fusarium graminearum.
Authors: Cao, H. / Walton, J.D. / Brumm, P. / Phillips, G.N.
History
DepositionNov 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-fucosidase GH29
B: Alpha-fucosidase GH29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,64623
Polymers131,4202
Non-polymers4,22621
Water25,2571402
1
A: Alpha-fucosidase GH29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,93412
Polymers65,7101
Non-polymers3,22411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-fucosidase GH29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,71211
Polymers65,7101
Non-polymers1,00210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.511, 75.512, 80.367
Angle α, β, γ (deg.)105.61, 107.19, 106.71
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alpha-fucosidase GH29


Mass: 65709.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium graminearum (fungus) / Gene: FCO1 / Production host: Pichia pastoris (fungus) / References: UniProt: J9UN47

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Sugars , 2 types, 5 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_d2-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#3: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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 , 4 types, 1418 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1402 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 293.15 K / Method: batch method / pH: 8
Details: 1:1 v/v mixture of 14-16 mg/ml alpha-L-fucosidase (stored in 25mM Tris pH 7.5 and partially deglycosylated by incubation 10:1:1 v/v ratio with EndoH and 500 mM sodium citrate pH 5.5 buffer ...Details: 1:1 v/v mixture of 14-16 mg/ml alpha-L-fucosidase (stored in 25mM Tris pH 7.5 and partially deglycosylated by incubation 10:1:1 v/v ratio with EndoH and 500 mM sodium citrate pH 5.5 buffer from New England Biolabs for more than 24hrs before setting up the drop) with 40% PEG 2000mme, 0.1M Tris pH 8.0, crystals grow within two days, cryoprotected by Mitegen LV cryo-oil, batch method, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2013
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.3993→37.931 Å / Num. all: 209440 / Num. obs: 198748 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16 Å2
Reflection shellResolution: 1.3993→1.42 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.557 / % possible all: 92

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
MD2diffractometer software from EMBL (with LS-CAT developed extensions)data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HL8 (peptide only)

1hl8


Resolution: 1.3993→37.931 Å / Occupancy max: 1 / Occupancy min: 0.21 / SU ML: 0.13 / σ(F): 1.99 / Phase error: 18.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1667 1905 0.96 %
Rwork0.1447 --
obs0.1449 198748 94.9 %
all-209440 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.8 Å2
Refinement stepCycle: LAST / Resolution: 1.3993→37.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9251 0 277 1402 10930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110125
X-RAY DIFFRACTIONf_angle_d1.24813824
X-RAY DIFFRACTIONf_dihedral_angle_d12.773746
X-RAY DIFFRACTIONf_chiral_restr0.0531442
X-RAY DIFFRACTIONf_plane_restr0.0071801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3993-1.43430.29281310.2212761X-RAY DIFFRACTION86
1.4343-1.47310.21581320.20413676X-RAY DIFFRACTION93
1.4731-1.51640.2311280.185513720X-RAY DIFFRACTION92
1.5164-1.56540.21031300.171913714X-RAY DIFFRACTION93
1.5654-1.62130.21721490.161913846X-RAY DIFFRACTION93
1.6213-1.68620.19881260.157714003X-RAY DIFFRACTION95
1.6862-1.7630.18531290.157214125X-RAY DIFFRACTION95
1.763-1.85590.19381410.155114231X-RAY DIFFRACTION96
1.8559-1.97220.1621320.147614342X-RAY DIFFRACTION97
1.9722-2.12440.17811470.143614335X-RAY DIFFRACTION97
2.1244-2.33820.18241380.14614449X-RAY DIFFRACTION97
2.3382-2.67650.17311420.15314544X-RAY DIFFRACTION98
2.6765-3.37170.17281410.138714571X-RAY DIFFRACTION99
3.3717-37.9450.11381390.121214526X-RAY DIFFRACTION98

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