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- PDB-9k1m: Crystal structure of xylanase inhibitor protein (OsXIP) from rice -

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Basic information

Entry
Database: PDB / ID: 9k1m
TitleCrystal structure of xylanase inhibitor protein (OsXIP) from rice
ComponentsXylanase inhibitor protein XIP
KeywordsPLANT PROTEIN / CARBOHYDRATE / HYDROLASE
Function / homology
Function and homology information


enzyme inhibitor activity / defense response to fungus / carbohydrate metabolic process / extracellular region
Similarity search - Function
Chitinase Cts1-like / : / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Xylanase inhibitor protein XIP
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsOhnuma, T. / Takeshita, D.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K05834 Japan
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Molecular arrangements that accompany binding of rice xylanase inhibitor protein OsXIP and the Rhizopus oryzae GH11 xylanase RXyn2.
Authors: Ohnuma, T. / Tanaka, J. / Ozaki, H. / Mitsui, K. / Tsujitsugu, D. / Okugawa, M. / Takeda, T. / Ihara, M. / Fukamizo, T. / Takeshita, D.
History
DepositionOct 16, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylanase inhibitor protein XIP


Theoretical massNumber of molelcules
Total (without water)31,3291
Polymers31,3291
Non-polymers00
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.348, 68.743, 81.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Xylanase inhibitor protein XIP / OsXIP / Class III chitinase homolog XIP


Mass: 31329.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: XIP, Os05g0247800, LOC_Os05g15880, OJ1037_G10.8, OsJ_17793
Production host: Escherichia coli (E. coli) / References: UniProt: Q5WMW5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M BIS-TRIS pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→40.6 Å / Num. obs: 161647 / % possible obs: 99.1 % / Redundancy: 6.6 % / CC1/2: 0.999 / Net I/σ(I): 15.46
Reflection shellResolution: 1.3→1.37 Å / Num. unique obs: 25158 / CC1/2: 0.696

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→40.567 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.179 7871 4.87 %
Rwork0.1657 --
obs0.1663 161647 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→40.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 0 244 2313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142125
X-RAY DIFFRACTIONf_angle_d1.3392877
X-RAY DIFFRACTIONf_dihedral_angle_d13.64765
X-RAY DIFFRACTIONf_chiral_restr0.11297
X-RAY DIFFRACTIONf_plane_restr0.009375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.33172250.33454641X-RAY DIFFRACTION89
1.3148-1.33030.27832910.28824812X-RAY DIFFRACTION94
1.3303-1.34650.29642470.25884998X-RAY DIFFRACTION97
1.3465-1.36350.25712760.24515051X-RAY DIFFRACTION97
1.3635-1.38150.22462540.23365111X-RAY DIFFRACTION99
1.3815-1.40040.26512590.2285187X-RAY DIFFRACTION99
1.4004-1.42040.20832590.21395119X-RAY DIFFRACTION100
1.4204-1.44160.22712780.20175125X-RAY DIFFRACTION100
1.4416-1.46410.21952900.20285167X-RAY DIFFRACTION100
1.4641-1.48810.20462480.19285137X-RAY DIFFRACTION100
1.4881-1.51380.1962640.1895172X-RAY DIFFRACTION100
1.5138-1.54130.21332720.18365174X-RAY DIFFRACTION100
1.5413-1.5710.20472610.17295181X-RAY DIFFRACTION100
1.571-1.6030.19162800.16495117X-RAY DIFFRACTION100
1.603-1.63790.20082680.16825203X-RAY DIFFRACTION100
1.6379-1.6760.1772590.16255172X-RAY DIFFRACTION100
1.676-1.71790.1692230.1585158X-RAY DIFFRACTION100
1.7179-1.76440.17622370.16295213X-RAY DIFFRACTION100
1.7644-1.81630.18182530.15875187X-RAY DIFFRACTION100
1.8163-1.87490.18712790.16425150X-RAY DIFFRACTION100
1.8749-1.94190.19772680.15865134X-RAY DIFFRACTION100
1.9419-2.01970.17252740.15745177X-RAY DIFFRACTION100
2.0197-2.11160.16072490.15245205X-RAY DIFFRACTION100
2.1116-2.22290.16852670.1525153X-RAY DIFFRACTION100
2.2229-2.36220.18272770.15375215X-RAY DIFFRACTION100
2.3622-2.54450.17222670.15085151X-RAY DIFFRACTION100
2.5445-2.80050.16012560.15115191X-RAY DIFFRACTION100
2.8005-3.20560.19512700.16195139X-RAY DIFFRACTION100
3.2056-4.03820.16172480.15375168X-RAY DIFFRACTION100
4.0382-40.5670.15712720.17325168X-RAY DIFFRACTION100

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