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

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Basic information

Entry
Database: PDB / ID: 3cuj
TitleCellulomonas fimi Xylanase/Cellulase Cex (Cf Xyn10A) in complex with sulfur substituted beta-1,4 xylopentaose.
ComponentsExo-beta-1,4-glucanase
KeywordsHYDROLASE / CEX / XYLANASE / Isofagomine inhibitor / TIM BARREL / CELLULOSE DEGRADATION / Glycosidase
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / polysaccharide binding / 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 / 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
thio-xylopentaose / Exoglucanase/xylanase / Beta-xylanase
Similarity search - Component
Biological speciesCellulomonas fimi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 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 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,0102
Polymers34,2671
Non-polymers7431
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.368, 85.368, 78.940
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-563-

HOH

21A-564-

HOH

31A-621-

HOH

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Components

#1: Protein Exo-beta-1,4-glucanase / 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: Polysaccharide beta-D-xylopyranose-(1-4)-4-thio-beta-D-xylopyranose-(1-4)-4-thio-beta-D-xylopyranose-(1-4)-4-thio- ...beta-D-xylopyranose-(1-4)-4-thio-beta-D-xylopyranose-(1-4)-4-thio-beta-D-xylopyranose-(1-4)-4-thio-beta-D-xylopyranose-(1-4)-4-thio-beta-D-xylopyranose / thio-xylopentaose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 742.849 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with S-glycosidic bond between monosaccharides
References: thio-xylopentaose
DescriptorTypeProgram
WURCS=2.0/1,5,4/[a212h-1b_1-5]/1-1-1-1-1/a4-b1*S*_b4-c1*S*_c4-d1*S*_d4-e1*S*WURCSPDB2Glycan 1.1.0
[][b-D-Xylp4SH]{[(4+S)][b-D-Xylp4SH]{[(4+S)][b-D-Xylp4SH]{[(4+S)][b-D-Xylp4SH]{[(4+S)][b-D-Xylp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.1 Å3/Da / Density % sol: 41.39 %
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: Jun 3, 2003
RadiationMonochromator: Osmic focusing optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 32678 / Num. obs: 31796 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 1.7→1.7 Å / % possible all: 0.86

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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: 1.7→18.76 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.831 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17 1597 5 %RANDOM
Rwork0.158 ---
obs0.158 31789 97.35 %-
all-32654 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→18.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2445 0 46 366 2857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222555
X-RAY DIFFRACTIONr_angle_refined_deg1.291.9543479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6775323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.75924.5120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.75115388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9961514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021966
X-RAY DIFFRACTIONr_nbd_refined0.1970.21339
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21787
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2307
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.223
X-RAY DIFFRACTIONr_mcbond_it0.6651.51620
X-RAY DIFFRACTIONr_mcangle_it1.07822524
X-RAY DIFFRACTIONr_scbond_it1.76531062
X-RAY DIFFRACTIONr_scangle_it2.8574.5955
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 110 -
Rwork0.317 2118 -
all-2228 -
obs--94.41 %

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