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- PDB-9l3p: Crystal structure of endo-processive xyloglucanase Xeg5A E285A fr... -

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Basic information

Entry
Database: PDB / ID: 9l3p
TitleCrystal structure of endo-processive xyloglucanase Xeg5A E285A from Aspergillus oryzae with GLLX/L
ComponentsGlycoside hydrolase superfamily
KeywordsHYDROLASE / Xyloglucanase / Complex
Function / homology
Function and homology information


glycogen biosynthetic process / beta-glucosidase activity / cellulose catabolic process / cell wall organization / cell surface / extracellular region
Similarity search - Function
Glycoside hydrolase, family 5, endoglucanase B / Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / : / Cellulase (glycosyl hydrolase family 5) / Glycoside hydrolase, family 5 / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
alpha-D-mannopyranose / Glycoside hydrolase superfamily
Similarity search - Component
Biological speciesAspergillus oryzae RIB40 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsNakamichi, Y. / Shimada, N. / Watanabe, M. / Fujii, T. / Matsuzawa, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Struct.Biol. / Year: 2025
Title: Structural insights into substrate recognition of tri-modular xyloglucanase from Aspergillus oryzae.
Authors: Nakamichi, Y. / Shimada, N. / Watanabe, M. / Fujii, T. / Yaoi, K. / Matsuzawa, T.
History
DepositionDec 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 25, 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: Glycoside hydrolase superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,9108
Polymers71,4421
Non-polymers4,4687
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint61 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.596, 116.463, 105.418
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein / Non-polymers , 2 types, 46 molecules A

#1: Protein Glycoside hydrolase superfamily / Xyloglucanase


Mass: 71441.750 Da / Num. of mol.: 1 / Mutation: E285A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae RIB40 (mold) / Gene: Ao3042_05083 / Production host: Komagataella pastoris (fungus) / References: UniProt: I8IVP5
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 6 types, 7 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: 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.: 1
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
#4: Polysaccharide beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)-[beta-D-glucopyranose-(1-4)]beta-D- ...beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)-[beta-D-glucopyranose-(1-4)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1387.204 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-2DXylpa1-6[DGlcpb1-4]DGlcpb1-4[DGalpb1-2DXylpa1-6]DGlcpb1-4[DXylpa1-6]DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,9,8/[a2122h-1a_1-5][a2122h-1b_1-5][a212h-1a_1-5][a2112h-1b_1-5]/1-2-2-2-3-4-3-4-3/a4-b1_a6-i1_b4-c1_b6-g1_c4-d1_c6-e1_e2-f1_g2-h1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}[(6+1)][a-D-Xylp]{[(2+1)][b-D-Galp]{}}}[(6+1)][a-D-Xylp]{[(2+1)][b-D-Galp]{}}}[(6+1)][a-D-Xylp]{}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 474.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-2DXylpa1-6DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a212h-1a_1-5][a2112h-1b_1-5]/1-2-3/a6-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(6+1)][a-D-Xylp]{[(2+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#6: 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.: 2 / 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
#7: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium acetate, 0.1 M bis-Tris methane, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: LN2 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.34→44.18 Å / Num. obs: 29373 / % possible obs: 99.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 47.06 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.065 / Net I/σ(I): 9.2
Reflection shellResolution: 2.34→2.43 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2839 / CC1/2: 0.523 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSJan 10, 2022data reduction
XDSJan 10, 2022data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→37.79 Å / SU ML: 0.337 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0904
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2154 1465 5 %
Rwork0.2059 27859 -
obs0.2064 29324 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.32 Å2
Refinement stepCycle: LAST / Resolution: 2.34→37.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4305 0 298 45 4648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01034750
X-RAY DIFFRACTIONf_angle_d1.14666505
X-RAY DIFFRACTIONf_chiral_restr0.1719809
X-RAY DIFFRACTIONf_plane_restr0.0066790
X-RAY DIFFRACTIONf_dihedral_angle_d20.71971905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.430.36391420.35532693X-RAY DIFFRACTION97.89
2.43-2.520.37011460.32122768X-RAY DIFFRACTION99.56
2.52-2.640.29241430.29412741X-RAY DIFFRACTION99.38
2.64-2.780.28651440.26832763X-RAY DIFFRACTION99.45
2.78-2.950.2631460.23472763X-RAY DIFFRACTION99.66
2.95-3.180.23651460.20962779X-RAY DIFFRACTION99.8
3.18-3.50.21061480.21712794X-RAY DIFFRACTION99.46
3.5-40.19761470.17272799X-RAY DIFFRACTION99.83
4.01-5.040.15091490.16262831X-RAY DIFFRACTION99.93
5.05-37.790.19161540.18422928X-RAY DIFFRACTION99.58
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)
14.65030686221.06359749553-3.136334953962.226529612560.9108551862535.73264823484-0.01006467181970.0601752197340.596537850731-0.274442207779-0.07270973597340.17924321616-0.4926055888510.02219478857030.1894257910550.4419664963580.0662655218907-0.09424246864570.3681401027590.07861469984880.339552455145-35.689533518-2.2043982422218.7844965452
21.086552782690.9067314792740.08053235506992.365191016780.3832685240321.22323904373-0.0186544701979-0.08994391659090.08190916370320.07622270384230.009617965920280.00843508274178-0.1597250598330.01823969084980.01758969640990.3883891079570.04771013497040.0004650002580660.2804395967880.01831211565660.279631262363-29.7785773202-11.040675038419.4552071804
33.06373776191-0.445713150972-0.2840932893391.103037571290.4003246783612.17326994177-0.01354431001040.130333774211-0.271184997401-0.03482171005120.03798503716830.0060715864270.1768484852580.162594371481-0.007490959523610.491057129543-0.0100528800337-0.01759730868030.276939195899-0.01670665005140.339759384719-33.6631322163-38.06647319083.59899199429
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 21 through 54 )21 - 541 - 34
22chain 'A' and (resid 55 through 353 )55 - 35335 - 333
33chain 'A' and (resid 354 through 569 )354 - 569334 - 549

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