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- PDB-1w9f: CBM29-2 mutant R112A: Probing the Mechanism of Ligand Recognition... -

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Basic information

Entry
Database: PDB / ID: 1w9f
TitleCBM29-2 mutant R112A: Probing the Mechanism of Ligand Recognition by Family 29 Carbohydrate Binding Modules
ComponentsNON CATALYTIC PROTEIN 1
KeywordsCARBOHYDRATE BINDING DOMAIN / 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: 2.25 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
DepositionOct 12, 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 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
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)33,1792
Polymers33,1792
Non-polymers00
Water1,47782
1
A: NON CATALYTIC PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)16,5891
Polymers16,5891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: NON CATALYTIC PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)16,5891
Polymers16,5891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.802, 91.802, 79.865
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-2024-

HOH

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Components

#1: Protein NON CATALYTIC PROTEIN 1


Mass: 16589.262 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.: 82 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE ARG 445 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 Å3/Da / Density % sol: 58.7 %
Crystal growpH: 7.5
Details: 100 MM NA/HEPES BUFFER PH 7.5, 150 MM KSCN, 20% ETHYLENE GLYCOL, 18% PEG3350

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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: 2.25→26 Å / Num. obs: 15514 / % possible obs: 92.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.1
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 3 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.6 / % possible all: 70.6

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Processing

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

1gwm


Resolution: 2.25→24.62 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 14.215 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 768 5 %RANDOM
Rwork0.204 ---
obs0.206 14706 92.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.25→24.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 0 82 2302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222274
X-RAY DIFFRACTIONr_bond_other_d0.0010.021953
X-RAY DIFFRACTIONr_angle_refined_deg1.6971.9313084
X-RAY DIFFRACTIONr_angle_other_deg0.85834561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3645282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26825.088114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.74315357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.817159
X-RAY DIFFRACTIONr_chiral_restr0.1010.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022595
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02476
X-RAY DIFFRACTIONr_nbd_refined0.1860.2398
X-RAY DIFFRACTIONr_nbd_other0.190.21890
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21048
X-RAY DIFFRACTIONr_nbtor_other0.0920.21401
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6960.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1611.51784
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42422247
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.06931062
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9064.5837
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: 2.25→2.31 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.393 32
Rwork0.304 750

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