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- PDB-2xyl: CELLULOMONAS FIMI XYLANASE/CELLULASE COMPLEXED WITH 2-DEOXY-2-FLU... -

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Basic information

Entry
Database: PDB / ID: 2xyl
TitleCELLULOMONAS FIMI XYLANASE/CELLULASE COMPLEXED WITH 2-DEOXY-2-FLUORO-XYLOBIOSE
ComponentsBETA-1,4-GLYCANASE
KeywordsHYDROLASE / O-GLYCOSYL / XYLANASE/CELLULASE / A/B BARREL / CELLULOSE DEGRADATION
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 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Exoglucanase/xylanase
Similarity search - Component
Biological speciesCellulomonas fimi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR SUBSTITUTION / Resolution: 1.9 Å
AuthorsMonem, V. / Birsan, C. / Warren, R.A.J. / Withers, S.G. / Rose, D.R.
CitationJournal: Biochemistry / Year: 1998
Title: Exploring the cellulose/xylan specificity of the beta-1,4-glycanase cex from Cellulomonas fimi through crystallography and mutation.
Authors: Notenboom, V. / Birsan, C. / Warren, R.A. / Withers, S.G. / Rose, D.R.
History
DepositionNov 20, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_initial_refinement_model / 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
Revision 2.2Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,3362
Polymers34,0521
Non-polymers2841
Water2,198122
1
A: BETA-1,4-GLYCANASE
hetero molecules

A: BETA-1,4-GLYCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6724
Polymers68,1042
Non-polymers5682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
Unit cell
Length a, b, c (Å)88.180, 88.180, 81.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein BETA-1,4-GLYCANASE / CEX / 1 / 4-BETA-CELLOBIOHYDROLASE


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: Polysaccharide beta-D-xylopyranose-(1-4)-2-deoxy-2-fluoro-alpha-D-xylopyranose


Type: oligosaccharide / Mass: 284.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a212h-1a_1-5_2*F][a212h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][<C5O2F1>]{[(1+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growpH: 4.6
Details: 7-10% PEG 4K, .1M NAACETATE PH4.6 60 MG/ML PROTEIN CONCENTRATION SOAK 48 HRS WITH 2F-XYLOBIOSE-DNP
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Bedarkar, S., (1992) J.Mol. Biol, 228, 693.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
165 mg/mlCex1dropin water
27.5-10 %PEG40001drop
30.1 Msodium acetate1drop
47.5-10 %PEG40001reservoir
50.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Apr 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 25857 / % possible obs: 99.94 % / Observed criterion σ(I): 2 / Redundancy: 7.64 % / Rsym value: 0.0803 / Net I/σ(I): 16.19
Reflection shellResolution: 1.9→2.05 Å / Redundancy: 5.06 % / Mean I/σ(I) obs: 3.58 / Rsym value: 0.2703 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 197626 / Rmerge(I) obs: 0.0803
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 99.9 % / Num. unique obs: 5050 / Num. measured obs: 25539 / Rmerge(I) obs: 0.2703

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR SUBSTITUTION
Starting model: PDB ENTRY 2EXO

2exo


Resolution: 1.9→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.0001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1756 7 %RANDOM
Rwork0.212 ---
obs0.212 25480 99.9 %-
Displacement parametersBiso mean: 13 Å2
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2399 0 0 0 2399
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.23
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.03
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.348 222 7.1 %
Rwork0.286 2881 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.03

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