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- PDB-1w8u: CBM29-2 mutant D83A complexed with mannohexaose: Probing the Mech... -

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Basic information

Entry
Database: PDB / ID: 1w8u
TitleCBM29-2 mutant D83A complexed with mannohexaose: Probing the Mechanism of Ligand Recognition by Family 29 Carbohydrate Binding Modules
ComponentsNON CATALYTIC PROTEIN 1
KeywordsCARBOHYDRATE-BINDING DOMAIN / CARBOHYDRATE BINDING MODULE / GLUCOMANNAN / CELLOHEXAOSE / MANNOHEXAOSE / CELLULOSOME
Function / homology
Function and homology information


Fungal dockerin domain superfamily / Cellulose or protein binding domain / CBM10/dockerin domain / CBM10 (carbohydrate-binding type-10) domain profile. / Galactose-binding lectin / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Non-catalytic protein 1
Similarity search - Component
Biological speciesPIROMYCES EQUI (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsFlint, J. / Bolam, D.N. / Nurizzo, D. / Taylor, E.J. / Williamson, M.P. / Walters, C. / Davies, G.J. / Gilbert, H.J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Probing the Mechanism of Ligand Recognition in Family 29 Carbohydrate-Binding Modules
Authors: Flint, J. / Bolam, D.N. / Nurizzo, D. / Taylor, E.J. / Williamson, M.P. / Walters, C. / Davies, G.J. / Gilbert, H.J.
History
DepositionSep 28, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
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: NON CATALYTIC PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4512
Polymers16,6221
Non-polymers8291
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.150, 42.636, 60.182
Angle α, β, γ (deg.)90.00, 93.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NON CATALYTIC PROTEIN 1


Mass: 16622.336 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING MODULE 2, RESIDUES 334-478 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PIROMYCES EQUI (fungus) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9C171
#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D- ...beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a1122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE ASP 415 ALA, CHAIN A

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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: 0.43 %
Crystal growpH: 6.5
Details: 1.5 M AMMONIUM SULPHATE, 0.1 M SODIUM CITRATE PH6.5 10 MM MANNOHEXAOSE 25% GLYCEROL, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.3→100 Å / Num. obs: 31892 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 32.4
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 6.6 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GWM

1gwm


Resolution: 1.3→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.345 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.175 1610 5.1 %RANDOM
Rwork0.161 ---
obs0.162 30250 99.8 %-
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: 8.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.01 Å2
2--0.11 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 56 166 1328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221215
X-RAY DIFFRACTIONr_bond_other_d0.0020.021030
X-RAY DIFFRACTIONr_angle_refined_deg1.9081.9861651
X-RAY DIFFRACTIONr_angle_other_deg3.3532408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3345140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7424.5961
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10615191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.839157
X-RAY DIFFRACTIONr_chiral_restr0.1070.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021309
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02247
X-RAY DIFFRACTIONr_nbd_refined0.1890.2182
X-RAY DIFFRACTIONr_nbd_other0.1920.2989
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2596
X-RAY DIFFRACTIONr_nbtor_other0.0990.2713
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.470.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.370.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4361.5897
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73921125
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6583610
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8014.5526
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: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.227 125
Rwork0.191 2191

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