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- PDB-1w0n: Structure of uncomplexed Carbohydrate Binding Domain CBM36 -

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Basic information

Entry
Database: PDB / ID: 1w0n
TitleStructure of uncomplexed Carbohydrate Binding Domain CBM36
ComponentsENDO-1,4-BETA-XYLANASE D
KeywordsHYDROLASE / CARBOHYDRATE-BINDING MODULE / CARBOHYDRATE BINDING / XYLAN / CBM36 / XYLANASE
Function / homology
Function and homology information


non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / xylan catabolic process / carbohydrate binding / extracellular region / metal ion binding
Similarity search - Function
Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily ...Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Arabinoxylan arabinofuranohydrolase
Similarity search - Component
Biological speciesPAENIBACILLUS POLYMYXA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 0.8 Å
AuthorsJamal, S. / Boraston, A.B. / Davies, G.J.
CitationJournal: Structure / Year: 2004
Title: Ab Initio Structure Determination and Functional Characterization of Cbm36: A New Family of Calcium-Dependent Carbohydrate Binding Modules
Authors: Jamal, S. / Boraston, A.B. / Turkenburg, J.P. / Tarbouriech, N. / Ducros, V.M.-A. / Davies, G.J.
History
DepositionJun 9, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)14,0424
Polymers13,8811
Non-polymers1603
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)30.529, 40.187, 81.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ENDO-1,4-BETA-XYLANASE D / 1 / 4-BETA-D-XYLAN XYLANOHYDROLASE D / XYLANASE D


Mass: 13881.170 Da / Num. of mol.: 1
Fragment: CARBOHYDRATE-BINDING MODULE 36 DOMAIN FROM XYLANASE 43A, RESIDUES 505-635
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PAENIBACILLUS POLYMYXA (bacteria) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P45796, endo-1,4-beta-xylanase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN TERMINAL RESIDUES DISORDERED

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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: 1.79 Å3/Da / Density % sol: 31.45 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: CRYSTALS OF NATIVE CBM36 (14.9 MG/ML) WERE GROWN USING THE VAPOR DIFFUSION TECHNIQUE FROM HANGING DROPS IN 1.6 M MAGNESIUM SULFATE AND 0.1 M MES, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 0.8→25 Å / Num. obs: 95183 / % possible obs: 97 % / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12
Reflection shellResolution: 0.8→0.84 Å / Redundancy: 2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 0.8→24.33 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.279 / SU ML: 0.008 / Cross valid method: THROUGHOUT / ESU R: 0.012 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.144 4987 5 %RANDOM
Rwork0.129 ---
obs0.129 95183 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2---0.31 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 0.8→24.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms895 0 7 206 1108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022971
X-RAY DIFFRACTIONr_bond_other_d0.0130.02838
X-RAY DIFFRACTIONr_angle_refined_deg2.0321.9251324
X-RAY DIFFRACTIONr_angle_other_deg3.87931967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1625125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87325.71442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06515153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.653151
X-RAY DIFFRACTIONr_chiral_restr0.1240.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021106
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02194
X-RAY DIFFRACTIONr_nbd_refined0.3420.2173
X-RAY DIFFRACTIONr_nbd_other0.2110.2824
X-RAY DIFFRACTIONr_nbtor_refined0.2470.2465
X-RAY DIFFRACTIONr_nbtor_other0.1280.2559
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2270.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1971.5628
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8042995
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.853394
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8494.5329
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.8→0.82 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.268 296
Rwork0.256 5431

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