[English] 日本語
Yorodumi
- PDB-1te1: Crystal structure of family 11 xylanase in complex with inhibitor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1te1
TitleCrystal structure of family 11 xylanase in complex with inhibitor (XIP-I)
Components
  • endo-1,4-xylanase
  • xylanase inhibitor protein I
KeywordsHYDROLASE INHIBITOR/HYDROLASE / BETA/ALPHA BARREL (XIP-I) and BETA JELLY ROLL (GH11) / HYDROLASE INHIBITOR-HYDROLASE COMPLEX
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 / enzyme inhibitor activity / defense response to fungus / carbohydrate metabolic process / extracellular region
Similarity search - Function
Chitinase Cts1-like / : / 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 ...Chitinase Cts1-like / : / 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 / Glycosyl hydrolases family 18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosidases / Concanavalin A-like lectin/glucanase domain superfamily / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Xylanase inhibitor protein 1 / Endo-1,4-beta-xylanase C
Similarity search - Component
Biological speciesPenicillium funiculosum (fungus)
Triticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPayan, F. / Leone, P. / Furniss, C. / Tahir, T. / Durand, A. / Porciero, S. / Manzanares, P. / Williamson, G. / Gilbert, H.J. / Juge, N. / Roussel, A.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Dual Nature of the Wheat Xylanase Protein Inhibitor XIP-I: STRUCTURAL BASIS FOR THE INHIBITION OF FAMILY 10 AND FAMILY 11 XYLANASES.
Authors: Payan, F. / Leone, P. / Porciero, S. / Furniss, C. / Tahir, T. / Williamson, G. / Durand, A. / Manzanares, P. / Gilbert, H.J. / Juge, N. / Roussel, A.
History
DepositionMay 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 23, 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE AUTHORS BELIEVE THAT THESE RESIDUES ARE CORRECT AND GENEBANK IS INCORRECT AT THESE ...SEQUENCE THE AUTHORS BELIEVE THAT THESE RESIDUES ARE CORRECT AND GENEBANK IS INCORRECT AT THESE POSITIONS (SEE PDB ENTRY 1OM0).

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: xylanase inhibitor protein I
B: endo-1,4-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,08315
Polymers50,9582
Non-polymers1,12513
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.748, 98.748, 112.095
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein xylanase inhibitor protein I / XIP-1


Mass: 30323.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / References: UniProt: Q8L5C6
#2: Protein endo-1,4-xylanase / GH11


Mass: 20633.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium funiculosum (fungus) / Gene: xynC / Production host: Penicillium funiculosum (fungus) / References: UniProt: Q9HFH0, endo-1,4-beta-xylanase
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, ammonium sulfate, 1,2,3-heptanetriol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9785 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 12, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 19734 / % possible obs: 99.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 60.5 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.068 / Net I/σ(I): 8.5
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 1.9 / Num. unique all: 2834 / Rsym value: 0.387 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UKR, PDB ENTRY 1OMO

1ukr

1omo


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.903 / SU B: 11.999 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 0.635 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27091 1428 7.3 %RANDOM
Rwork0.20844 ---
all0.21 ---
obs0.21288 18253 99.74 %-
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: 26.836 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å20 Å2
2---1.45 Å20 Å2
3---2.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3603 0 72 199 3874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213777
X-RAY DIFFRACTIONr_bond_other_d0.0020.023153
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.9315127
X-RAY DIFFRACTIONr_angle_other_deg1.00537340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.525462
X-RAY DIFFRACTIONr_chiral_restr0.0680.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024266
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02818
X-RAY DIFFRACTIONr_nbd_refined0.1790.2824
X-RAY DIFFRACTIONr_nbd_other0.2170.23796
X-RAY DIFFRACTIONr_nbtor_other0.0860.22131
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2153
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.160.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2850.27
X-RAY DIFFRACTIONr_mcbond_it0.3671.52281
X-RAY DIFFRACTIONr_mcangle_it0.723648
X-RAY DIFFRACTIONr_scbond_it1.09731496
X-RAY DIFFRACTIONr_scangle_it1.994.51479
LS refinement shellResolution: 2.5→2.633 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.356 228
Rwork0.289 2567
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)
12.63661.28571.09125.72230.70581.962-0.165-0.1853-0.1937-0.31810.2619-0.0925-0.2693-0.2105-0.0970.30070.05260.05690.22950.14840.097823.17157.31846.831
21.46731.0046-0.37676.9264-1.57532.3987-0.0611-0.2266-0.0451.75230.2763-0.4968-0.4417-0.0006-0.21520.87730.1809-0.09460.2512-0.05550.118933.29285.23859.965
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2741 - 274
2X-RAY DIFFRACTION2BB0 - 1891 - 190

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more