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- PDB-1fh7: CRYSTAL STRUCTURE OF THE XYLANASE CEX WITH XYLOBIOSE-DERIVED INHI... -

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Basic information

Entry
Database: PDB / ID: 1fh7
TitleCRYSTAL STRUCTURE OF THE XYLANASE CEX WITH XYLOBIOSE-DERIVED INHIBITOR DEOXYNOJIRIMYCIN
ComponentsBETA-1,4-XYLANASE
KeywordsHYDROLASE / cex / xylanase / deoxynojirimycin inhibitor / cellulose degradation
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / polysaccharide binding / endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process / cellulose catabolic process
Similarity search - Function
Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. ...Carbohydrate-binding type-2, conserved site / CBM2a (carbohydrate-binding type-2) domain signature. / Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PIPERIDINE-3,4,5-TRIOL / beta-D-xylopyranose / : / Exoglucanase/xylanase
Similarity search - Component
Biological speciesCellulomonas fimi (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.82 Å
AuthorsNotenboom, V. / Williams, S.J. / Hoos, R. / Withers, S.G. / Rose, D.R.
CitationJournal: Biochemistry / Year: 2000
Title: Detailed structural analysis of glycosidase/inhibitor interactions: complexes of Cex from Cellulomonas fimi with xylobiose-derived aza-sugars.
Authors: Notenboom, V. / Williams, S.J. / Hoos, R. / Withers, S.G. / Rose, D.R.
History
DepositionJul 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-1,4-XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3353
Polymers34,0521
Non-polymers2832
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.040, 87.040, 80.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1037-

HOH

21A-1099-

HOH

31A-1104-

HOH

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Components

#1: Protein BETA-1,4-XYLANASE / CEX


Mass: 34051.941 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellulomonas fimi (bacteria) / Production host: Escherichia coli (E. coli)
References: GenBank: 144429, UniProt: P07986*PLUS, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-XDN / PIPERIDINE-3,4,5-TRIOL / XYLOSE-DERIVED 1-DEOXY-NOJIRIMYCIN


Mass: 133.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H11NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG4K 15%, NaAcetate 0.1 M, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: Bedarkar, S., (1992) J.Mol. Biol, 228, 693.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
165 mg/mlCex1drop
27.5-10 %PEG40001drop
30.1 Msodium acetate1drop
47.5-10 %PEG40001reservoir
50.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. all: 519114 / Num. obs: 27874 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 15 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 14.7
Reflection shellResolution: 1.82→1.9 Å / Redundancy: 7 % / Rmerge(I) obs: 0.246 / Num. unique all: 27874 / % possible all: 97.4
Reflection shell
*PLUS
% possible obs: 97.4 % / Mean I/σ(I) obs: 6.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 1.82→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 509339.8 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2747 9.9 %RANDOM
Rwork0.21 ---
all0.21 519114 --
obs0.21 27663 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.81 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.83 Å20 Å20 Å2
2--1.83 Å20 Å2
3----3.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.82→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 18 268 2686
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.82→1.93 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 443 10.1 %
Rwork0.288 3927 -
obs--94.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM3.CHOTOPH3.CHO
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4CIS-THR81.PEP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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