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- PDB-9l3d: Crystal structure of endo-processive xyloglucanase Xeg5A from Asp... -

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Basic information

Entry
Database: PDB / ID: 9l3d
TitleCrystal structure of endo-processive xyloglucanase Xeg5A from Aspergillus oryzae
ComponentsGlycoside hydrolase superfamily
KeywordsHYDROLASE / Xyloglucanase / Glycoside hydrolase family 5
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 / : / Glycoside hydrolase, family 5 / Cellulase (glycosyl 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: 1.9 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 18, 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
B: Glycoside hydrolase superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,02131
Polymers143,0002
Non-polymers12,02129
Water16,069892
1
A: Glycoside hydrolase superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,65918
Polymers71,5001
Non-polymers6,16017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint96 kcal/mol
Surface area23990 Å2
MethodPISA
2
B: Glycoside hydrolase superfamily
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,36113
Polymers71,5001
Non-polymers5,86112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint102 kcal/mol
Surface area24050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.038, 119.841, 106.445
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycoside hydrolase superfamily / GH5 xyloglucanase


Mass: 71499.789 Da / Num. of mol.: 2
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

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Sugars , 7 types, 14 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-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)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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: 1397.245 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1WURCSPDB2Glycan 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]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1721.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2[DManpa1-6]DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-h1_d2-e1_d6-g1_e2-f1_h3-i1_h6-j1WURCSPDB2Glycan 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]{}}[(6+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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.: 2 / 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
#8: 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.: 4 / 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 , 2 types, 907 molecules

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


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 892 / 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: 2.61 Å3/Da / Density % sol: 52.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 25% PEG1500 and 0.1 M MMT buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→48.64 Å / Num. obs: 117783 / % possible obs: 99.35 % / Redundancy: 4.6 % / Biso Wilson estimate: 21.71 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.091 / Rrim(I) all: 0.198 / Net I/σ(I): 6.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.311 / Mean I/σ(I) obs: 1 / Num. unique obs: 11588 / CC1/2: 0.575 / Rpim(I) all: 0.712 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSJan 10, 2022data reduction
XDSJan 10, 2022data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.64 Å / SU ML: 0.2388 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.4906
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2492 5881 5 %
Rwork0.2156 111678 -
obs0.2173 117559 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.29 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8618 0 799 892 10309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00839670
X-RAY DIFFRACTIONf_angle_d0.926913208
X-RAY DIFFRACTIONf_chiral_restr0.05461658
X-RAY DIFFRACTIONf_plane_restr0.00751582
X-RAY DIFFRACTIONf_dihedral_angle_d8.1651698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.37731840.34963513X-RAY DIFFRACTION94.77
1.92-1.940.36061930.36123643X-RAY DIFFRACTION98.41
1.94-1.970.35881930.34133677X-RAY DIFFRACTION99.13
1.97-1.990.34081950.33293695X-RAY DIFFRACTION99.31
1.99-2.020.31991940.32013686X-RAY DIFFRACTION99.31
2.02-2.050.35961950.30033688X-RAY DIFFRACTION99.39
2.05-2.070.30361930.29623685X-RAY DIFFRACTION99.67
2.07-2.110.32371960.2853718X-RAY DIFFRACTION99.72
2.11-2.140.30761960.2783734X-RAY DIFFRACTION99.77
2.14-2.170.3021950.27673688X-RAY DIFFRACTION99.67
2.17-2.210.29631950.26563709X-RAY DIFFRACTION99.64
2.21-2.250.27231950.24913696X-RAY DIFFRACTION99.56
2.25-2.290.28231970.24543726X-RAY DIFFRACTION99.54
2.29-2.340.30771940.24623694X-RAY DIFFRACTION99.67
2.34-2.390.28841960.24033726X-RAY DIFFRACTION99.49
2.39-2.450.29711940.23883696X-RAY DIFFRACTION99.41
2.45-2.510.30011960.22473714X-RAY DIFFRACTION99.44
2.51-2.580.24841950.22363710X-RAY DIFFRACTION99.41
2.58-2.650.24441960.21693714X-RAY DIFFRACTION99.34
2.65-2.740.29471930.21723681X-RAY DIFFRACTION98.37
2.74-2.840.24951980.21643737X-RAY DIFFRACTION99.7
2.84-2.950.24161960.20843747X-RAY DIFFRACTION99.82
2.95-3.080.22691980.20493767X-RAY DIFFRACTION99.87
3.08-3.250.26531990.19333757X-RAY DIFFRACTION99.8
3.25-3.450.19931960.18773752X-RAY DIFFRACTION99.67
3.45-3.720.22511990.16613774X-RAY DIFFRACTION99.85
3.72-4.090.17612000.16143796X-RAY DIFFRACTION99.73
4.09-4.680.19082000.14253796X-RAY DIFFRACTION99.35
4.68-5.90.17512010.16193803X-RAY DIFFRACTION98.5
5.9-48.640.19992090.18953956X-RAY DIFFRACTION98.3
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)
11.084823314120.1629988815910.5057146250721.701014884181.449239298272.26402384303-0.0422112923854-0.03698231767460.0916570873950.06629802118630.049447086308-0.132946931428-0.01143470329530.174707637196-0.04255482048770.194334055750.009074867844760.003430414644840.31186710579-0.03207229877760.225020481434-13.260692231437.1757850891-7.54043751564
21.03231597641-0.07496357434030.2336138272240.368125383717-0.2194401336620.791717070472-0.00439651049671-0.04928582753520.006721367987980.028470950122-0.0139978480362-0.03936938247660.02009173644350.08682001635770.02104970462280.1460753409340.005790455399070.003832174685180.188081467351-0.08216069571080.204682358555-21.991067792531.2356867413-7.02289045208
30.9456088748120.1102652532910.1440458641910.603979197382-0.1450078439160.893668692436-0.02119813162290.03523397284840.144860410418-0.0374808658819-0.0274904606299-0.0163336275704-0.0333874181572-0.1432478185670.04616155111990.2008372895990.0179676270592-0.007609199891710.123963451939-0.07956612656390.283448784343-48.524974273945.624037411-24.2064048171
40.473748075543-0.170137936437-0.007177923693720.187313849730.3459572016611.619272393470.0428612601246-0.123732008218-0.104503364077-0.100229435879-0.05426491518160.06596606020750.223599799944-0.004310913029390.01885053581090.2424542523170.01958939799840.004578332625060.113445806748-0.06521988623770.335880499062-49.811078116122.3191347743-21.5120731467
51.14091620276-0.4784600989280.6717378734432.00630027463-1.497729111072.12815384491-0.122903191052-0.2106599891380.0195354341705-0.000316054390730.06074933027270.145560898549-0.0902093018483-0.2224749875360.03289277747330.192925882170.01946256387450.02029060612190.320456429088-0.1302629411050.251510259129-8.581828085337.0317064123-45.3555483422
61.158467055940.2714633599610.1026288801410.464335341974-0.06734984717540.610273302421-0.0231898607136-0.00870041668046-0.00807434788626-0.03768400872860.01666023741610.02741243717350.0188961431840.004416807072630.004248406558340.16691344920.0101444785954-0.0020112745150.310611542985-0.08087804425250.2200452854050.16751353137831.279557322-46.1604250416
70.3608194738120.02698348173390.02092477648781.01683058625-0.003268236337270.415484283151-0.0260433988892-0.01234128046950.01322945694750.03940368910030.033718832463-0.05906563058910.01148856425520.00593885238937-0.006285035146780.16743585621-0.0139840295787-0.0138390760360.390761618995-0.08461822859810.24885731610327.405249378835.5097111271-30.2665870141
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 21 through 54 )AA21 - 541 - 34
22chain 'A' and (resid 55 through 353 )AA55 - 35335 - 333
33chain 'A' and (resid 354 through 478 )AA354 - 478334 - 458
44chain 'A' and (resid 479 through 569 )AA479 - 569459 - 549
55chain 'B' and (resid 21 through 54 )BD21 - 541 - 34
66chain 'B' and (resid 55 through 353 )BD55 - 35335 - 333
77chain 'B' and (resid 354 through 569 )BD354 - 569334 - 549

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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