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- PDB-1w8w: CBM29-2 mutant Y46A: Probing the Mechanism of Ligand Recognition ... -

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Basic information

Entry
Database: PDB / ID: 1w8w
TitleCBM29-2 mutant Y46A: 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: 2.1 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 30, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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

Downloads & links

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Assembly

Deposited unit
A: NON-CATALYTIC PROTEIN 1
B: NON-CATALYTIC PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)33,1492
Polymers33,1492
Non-polymers00
Water1,60389
1
A: NON-CATALYTIC PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)16,5741
Polymers16,5741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: NON-CATALYTIC PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)16,5741
Polymers16,5741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)92.485, 92.485, 80.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-2022-

HOH

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Components

#1: Protein NON-CATALYTIC PROTEIN 1


Mass: 16574.250 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE TYR 379 ALA, CHAIN A AND CHAIN B

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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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 7.5
Details: 100 MM NA/HEPES BUFFER PH 7.5, CONTAINING 150 MM KSCN, 20% ETHYLENE GLYCOL 20%PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 21019 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.11refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GWM

1gwm


Resolution: 2.1→65.94 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.405 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1080 5.1 %RANDOM
Rwork0.2 ---
obs0.202 19941 99.9 %-
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: 19.63 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å20 Å2
2---1.22 Å20 Å2
3---2.43 Å2
Refinement stepCycle: LAST / Resolution: 2.1→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 0 89 2332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212294
X-RAY DIFFRACTIONr_bond_other_d0.0020.021970
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9333109
X-RAY DIFFRACTIONr_angle_other_deg1.44534593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5475284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94424.746118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.40615361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0381512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022624
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02486
X-RAY DIFFRACTIONr_nbd_refined0.1940.2380
X-RAY DIFFRACTIONr_nbd_other0.2590.22147
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.21364
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.268
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3280.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.360.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6871.51410
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26722264
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2043884
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3844.5845
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.291 73
Rwork0.251 1469
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.95960.8534-0.86134.10180.78462.83480.0833-0.3908-0.0690.3555-0.15610.04270.05870.02450.07280.1216-0.0173-0.0090.07650.06570.0567-26.5607-0.825444.9679
23.1654-0.39060.05942.53840.05923.79910.05860.22930.2527-0.301-0.04320.2286-0.1641-0.2189-0.01540.11960.0118-0.02630.0509-0.00860.1015-37.8135-22.609426.1676
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 149
2X-RAY DIFFRACTION2B4 - 143

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