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- PDB-1nae: Structure of CsCBM6-3 from Clostridium stercorarium in complex wi... -

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Basic information

Entry
Database: PDB / ID: 1nae
TitleStructure of CsCBM6-3 from Clostridium stercorarium in complex with xylotriose
Componentsputative xylanase
KeywordsHYDROLASE / carbohydrate-binding module / beta-sandwich / xylan / xylooligosaccharide
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / cellulose 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) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 ...Cellulose binding, type IV / Cellulose Binding Domain Type IV / Carbohydrate binding module (family 6) / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
4beta-beta-xylotriose / : / Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesClostridium stercorarium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBoraston, A.B. / Notenboom, V. / Warren, R.A.J. / Kilburn, D.G. / Rose, D.R. / Davies, G.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structure and ligand binding of carbohydrate-binding module CsCBM6-3 reveals similarities with fucose-specific lectins and "galactose-binding" domains
Authors: Boraston, A.B. / Notenboom, V. / Warren, R.A.J. / Kilburn, D.G. / Rose, D.R. / Davies, G.
History
DepositionNov 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 / Database references / Derived calculations / 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 / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_asym_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.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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 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_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: putative xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8603
Polymers17,4061
Non-polymers4542
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.648, 49.746, 36.082
Angle α, β, γ (deg.)90.00, 93.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein putative xylanase /


Mass: 17405.947 Da / Num. of mol.: 1 / Fragment: C-terminal carbohydrate-binding module
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium stercorarium (bacteria) / Gene: putative xylanase / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: GenBank: 16076818, UniProt: Q8GJ44*PLUS
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 414.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylotriose
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a212h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 1.63 Å3/Da / Density % sol: 24.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 26%PEG 4K, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117 mg/mlprotein1drop
226 %(w/v)PEG40001reservoir
30.1 Msodium acetate1reservoirpH4.6
40.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 12, 2002 / Details: long mirror focused
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→36.04 Å / Num. all: 6680 / Num. obs: 6382 / Redundancy: 2.3 % / Biso Wilson estimate: 20.33 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 12.4
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 5.4 / Num. unique all: 649 / Rsym value: 0.186
Reflection
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 40 Å / % possible obs: 94.6 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 2.36 Å / % possible obs: 72.1 % / Redundancy: 5 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 6.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gmm

1gmm


Resolution: 2.05→36.04 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.63 / SU ML: 0.126 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.194
RfactorNum. reflection% reflectionSelection details
Rfree0.19487 279 4.8 %RANDOM
Rwork0.1345 ---
all0.13748 ---
obs0.13748 5544 87.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.907 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å2-0.1 Å2
2---0.04 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.05→36.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms952 0 29 181 1162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211001
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9661367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.155128
X-RAY DIFFRACTIONr_chiral_restr0.1030.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02747
X-RAY DIFFRACTIONr_nbd_refined0.210.2443
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2141
X-RAY DIFFRACTIONr_metal_ion_refined0.0990.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.231
X-RAY DIFFRACTIONr_mcbond_it0.7711.5631
X-RAY DIFFRACTIONr_mcangle_it1.35321015
X-RAY DIFFRACTIONr_scbond_it2.2763370
X-RAY DIFFRACTIONr_scangle_it3.1324.5352
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.295 28
Rwork0.167 416
obs-648
Refinement
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.203 / Rfactor Rwork: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.58
LS refinement shell
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 2.36 Å

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