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- PDB-1uz0: Carbohydrate binding module (CBM6cm-2) from Cellvibrio mixtus lic... -

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Basic information

Entry
Database: PDB / ID: 1uz0
TitleCarbohydrate binding module (CBM6cm-2) from Cellvibrio mixtus lichenase 5A in complex with Glc-4Glc-3Glc-4Glc
ComponentsCELLULASE B
KeywordsCARBOHYDRATE BINDING MODULE / CBM6 / MIXED BETA1 / 3-1 / 4 LINKED GLUCAN
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / 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 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding domain-like ...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 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCELLVIBRIO MIXTUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCzjzek, M. / Pires, V.M.R. / Henshaw, J. / Prates, J.A.M. / Bolam, D. / Henrissat, B. / Gilbert, H.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Crystal Structure of the Family 6 Carbohydrate Binding Module from Cellvibrio Mixtus Endoglucanase 5A in Complex with Oligosaccharides Reveals Two Distinct Binding Sites with Different Ligand Specificities
Authors: Pires, V.M.R. / Henshaw, J. / Prates, J.A.M. / Bolam, D. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Henrissat, B. / Planas, A. / Gilbert, H.J. / Czjzek, M.
History
DepositionMar 3, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / 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_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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _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_auth_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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELLULASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6416
Polymers13,7671
Non-polymers8745
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)37.924, 102.410, 31.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2059-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein CELLULASE B


Mass: 13766.938 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 493-622
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CELLVIBRIO MIXTUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O07653
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-3DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b3-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 132 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growpH: 7 / Details: 11% PEG 6000, 2.0 M NACL, pH 7.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
212 %(w/v)PEG60001reservoir
32.2 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorDate: Nov 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.9→24.3 Å / Num. obs: 10234 / % possible obs: 99.6 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 4.5
Reflection shellResolution: 1.9→1.98 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.3 / % possible all: 99
Reflection
*PLUS
Highest resolution: 1.9 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.112
Reflection shell
*PLUS
% possible obs: 99 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GMM

1gmm


Resolution: 2→51.3 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.991 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.209 423 4.8 %RANDOM
Rwork0.15 ---
obs0.152 8391 99.3 %-
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: 9.52 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20 Å20 Å2
2--0.28 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2→51.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms973 0 54 128 1155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211050
X-RAY DIFFRACTIONr_bond_other_d0.0030.02867
X-RAY DIFFRACTIONr_angle_refined_deg1.7591.9471437
X-RAY DIFFRACTIONr_angle_other_deg0.98832019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4485130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.021158
X-RAY DIFFRACTIONr_gen_planes_other0.030.02195
X-RAY DIFFRACTIONr_nbd_refined0.210.2159
X-RAY DIFFRACTIONr_nbd_other0.2740.21027
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.2580
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.090.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5390.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0391.5639
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73321018
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6683411
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6354.5419
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: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.196 33
Rwork0.144 578
Refinement
*PLUS
Highest resolution: 1.9 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.149
Solvent computation
*PLUS
Displacement parameters
*PLUS

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