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- PDB-3cuh: Cellulomonas fimi Xylanase/Cellulase Cex (Cf Xyn10A) in complex w... -

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Basic information

Entry
Database: PDB / ID: 3cuh
TitleCellulomonas fimi Xylanase/Cellulase Cex (Cf Xyn10A) in complex with cellotriose-like isofagomine
ComponentsExo-beta-1,4-glucanaseGlucan 1,4-beta-glucosidase
KeywordsHYDROLASE / CEX / XYLANASE / Isofagomine inhibitor / TIM BARREL / Glycosidase
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 activity / endo-1,4-beta-xylanase / 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. / Glycoside hydrolase family 10 ...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. / Glycoside hydrolase family 10 / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / CBM2/CBM3, carbohydrate-binding domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-G2I / Exoglucanase/xylanase / Beta-xylanase
Similarity search - Component
Biological speciesCellulomonas fimi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å
AuthorsKuntz, D.A. / Saul, M. / Rose, D.R.
CitationJournal: to be published
Title: Probing the binding sites of Family 10 and 11 Xylanases with extended Oligosaccharides
Authors: Poon, D.K.Y. / D'Angelo, I.D. / Kuntz, D.A. / Kantner, T. / Ludkiwzek, M.L. / Tarling, C. / Rose, D.R. / Saul, M. / McIntosh, L.P. / Withers, S.G.
History
DepositionApr 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Exo-beta-1,4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7392
Polymers34,2671
Non-polymers4711
Water7,008389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.217, 86.217, 79.413
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-483-

HOH

21A-486-

HOH

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Components

#1: Protein Exo-beta-1,4-glucanase / Glucan 1,4-beta-glucosidase / Cellulomonas fimi Family 10 Xylanase/Cellulase / beta 1 / 4 endo-xylanase / Cex / Cf Xyn10A


Mass: 34267.148 Da / Num. of mol.: 1 / Fragment: sequence database residues 43-357
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellulomonas fimi (bacteria) / Gene: cex / Plasmid: pUC12 / Production host: Escherichia coli (E. coli)
References: UniProt: Q59277, UniProt: P07986*PLUS, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#2: Chemical ChemComp-G2I / (3R,4R,5R)-3-hydroxy-5-(hydroxymethyl)piperidin-4-yl 4-O-beta-D-glucopyranosyl-beta-D-glucopyranoside / Cellotriose-like isofagomine / Cellobiosyl isofagomine


Mass: 471.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H33NO13
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 389 / 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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 29, 2003
RadiationMonochromator: Osmic focussing optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.87→30 Å / Num. all: 25315 / Num. obs: 25315 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 21 % / Rmerge(I) obs: 0.05 / Χ2: 1.003 / Net I/σ(I): 22.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.87-1.910.25816580.923100
1.91-1.960.17716571.012100
1.96-2.010.14816411.046100
2.01-2.070.11816471.037100
2.07-2.140.10316681.062100
2.14-2.220.09216701.0599.9
2.22-2.310.08116441.035100
2.31-2.410.07416740.92100
2.41-2.540.06516831.087100
2.54-2.70.05716751.159100
2.7-2.90.0516890.996100
2.9-3.20.04216981.018100
3.2-3.660.03517110.959100
3.66-4.610.02917360.874100
4.61-300.02518640.865100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2EXO

2exo


Resolution: 1.89→19.99 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.348 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.181 1865 7.6 %RANDOM
Rwork0.148 ---
obs0.15 24512 100 %-
all-24512 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.271 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.89→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 32 392 2841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222507
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.943406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9955315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.61424.5120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10715380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5881514
X-RAY DIFFRACTIONr_chiral_restr0.0890.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021934
X-RAY DIFFRACTIONr_nbd_refined0.1980.21239
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21741
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2337
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.229
X-RAY DIFFRACTIONr_mcbond_it0.7221.51603
X-RAY DIFFRACTIONr_mcangle_it1.09222480
X-RAY DIFFRACTIONr_scbond_it1.81431044
X-RAY DIFFRACTIONr_scangle_it2.8674.5926
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 143 -
Rwork0.175 1598 -
all-1741 -
obs--100 %

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