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- PDB-1t6g: Crystal structure of the Triticum aestivum xylanase inhibitor-I i... -

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Basic information

Entry
Database: PDB / ID: 1t6g
TitleCrystal structure of the Triticum aestivum xylanase inhibitor-I in complex with aspergillus niger xylanase-I
Components
  • Endo-1,4-beta-xylanase IXylanase
  • xylanase inhibitor
KeywordsHYDROLASE INHIBITOR / protein-protein complex / two beta-barrel domain structure / beta-jelly roll structure
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / aspartic-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Xylanase inhibitor, C-terminal / Xylanase inhibitor I-like / Xylanase inhibitor C-terminal / Xylanase inhibitor, N-terminal / Xylanase inhibitor N-terminal / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. ...Xylanase inhibitor, C-terminal / Xylanase inhibitor I-like / Xylanase inhibitor C-terminal / Xylanase inhibitor, N-terminal / Xylanase inhibitor N-terminal / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Concanavalin A-like lectin/glucanase domain superfamily / Aspartic peptidase domain superfamily / Jelly Rolls / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase A / Xylanase inhibitor
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
Aspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSansen, S. / De Ranter, C.J. / Gebruers, K. / Brijs, K. / Courtin, C.M. / Delcour, J.A. / Rabijns, A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural basis for inhibition of Aspergillus niger xylanase by triticum aestivum xylanase inhibitor-I
Authors: Sansen, S. / De Ranter, C.J. / Gebruers, K. / Brijs, K. / Courtin, C.M. / Delcour, J.A. / Rabijns, A.
History
DepositionMay 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: xylanase inhibitor
B: xylanase inhibitor
C: Endo-1,4-beta-xylanase I
D: Endo-1,4-beta-xylanase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,8818
Polymers117,5134
Non-polymers3684
Water19,3481074
1
A: xylanase inhibitor
C: Endo-1,4-beta-xylanase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9414
Polymers58,7572
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-7 kcal/mol
Surface area21260 Å2
MethodPISA
2
B: xylanase inhibitor
D: Endo-1,4-beta-xylanase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9414
Polymers58,7572
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-7 kcal/mol
Surface area21330 Å2
MethodPISA
3
A: xylanase inhibitor
C: Endo-1,4-beta-xylanase I
hetero molecules

B: xylanase inhibitor
D: Endo-1,4-beta-xylanase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,8818
Polymers117,5134
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-y,x-y-1,z-1/31
Buried area6750 Å2
ΔGint-23 kcal/mol
Surface area40530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.434, 88.434, 128.995
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein xylanase inhibitor


Mass: 38862.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: purified from wheat flour / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8H0K8, endo-1,4-beta-xylanase
#2: Protein Endo-1,4-beta-xylanase I / Xylanase / Xylanase I / 1 / 4-beta-D-xylan xylanohydrolase I


Mass: 19893.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Aspergillus niger (mold) / References: UniProt: P55329, endo-1,4-beta-xylanase
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1074 / 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: 2.58 Å3/Da / Density % sol: 51.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.25 M magnesium acetate 0.1 M sodium cacodylate buffer, 17% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 4, 2002
RadiationMonochromator: Sagitally focusing Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→29.74 Å / Num. all: 104587 / Num. obs: 93187 / % possible obs: 89.1 % / Observed criterion σ(F): 1.41 / Observed criterion σ(I): 2
Reflection shellResolution: 1.8→1.9 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T6E, 1UKR
Resolution: 1.8→29.74 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.02 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19171 10511 10.1 %RANDOM
Rwork0.15828 ---
all0.16068 94039 --
obs0.16161 94039 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.576 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.05 Å20 Å2
2--0.11 Å20 Å2
3----0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.07 Å0.01 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8044 0 24 1074 9142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0218286
X-RAY DIFFRACTIONr_bond_other_d0.0020.027254
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.95411340
X-RAY DIFFRACTIONr_angle_other_deg0.78316888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8951092
X-RAY DIFFRACTIONr_chiral_restr0.0820.21270
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029446
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021664
X-RAY DIFFRACTIONr_nbd_refined0.1990.21450
X-RAY DIFFRACTIONr_nbd_other0.2530.28385
X-RAY DIFFRACTIONr_nbtor_other0.0830.24786
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2811
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3460.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3390.257
X-RAY DIFFRACTIONr_mcbond_it0.6391.55450
X-RAY DIFFRACTIONr_mcangle_it1.17728734
X-RAY DIFFRACTIONr_scbond_it1.82732836
X-RAY DIFFRACTIONr_scangle_it2.8914.52606
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.212 772
Rwork0.156 6936
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.093-0.03310.00620.2352-0.02440.1253-0.00920.00290.01790.01460.00890.0111-0.02640.00260.00030.01560.0045-0.00480.00320.00070.010643.105611.38970.3859
20.09320.0333-0.00150.2368-0.02390.1303-0.0076-0.0044-0.0174-0.01510.00930.01180.02660.0016-0.00170.0146-0.00420.00410.00380.00050.010443.1062-62.446515.6373
30.20510.04640.0680.14010.06860.1573-0.0117-0.01190.0095-0.002-0.01320.01890.0014-0.01970.02490.0061-0.0018-0.00580.0167-0.00290.008429.6998-15.6066-14.0369
40.2026-0.0522-0.05620.1370.07530.1473-0.00910.0123-0.01040.0008-0.01410.0174-0.0028-0.01850.02320.0060.00120.00670.0175-0.00280.008629.7025-35.439530.056
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3811 - 381
2X-RAY DIFFRACTION2BB1 - 3811 - 381
3X-RAY DIFFRACTION3CC2 - 1832 - 183
4X-RAY DIFFRACTION4DD2 - 1832 - 183

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