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

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Basic information

Entry
Database: PDB / ID: 1uxz
TitleCarbohydrate binding module (CBM6cm-2) from Cellvibrio mixtus lichenase 5A
ComponentsCELLULASE B
KeywordsCARBOHYDRATE BINDING MODULE / CBM6 / MIXTED 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: 1.4 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 1, 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 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELLULASE B
B: CELLULASE B


Theoretical massNumber of molelcules
Total (without water)27,5342
Polymers27,5342
Non-polymers00
Water7,044391
1
A: CELLULASE B


Theoretical massNumber of molelcules
Total (without water)13,7671
Polymers13,7671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CELLULASE B


Theoretical massNumber of molelcules
Total (without water)13,7671
Polymers13,7671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.110, 66.956, 85.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.08549, -0.99599, 0.02622), (0.99616, -0.08594, -0.01661), (0.01879, 0.0247, 0.99952)
Vector: 83.88921, -11.37161, -22.91246)

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Components

#1: Protein CELLULASE B


Mass: 13766.938 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 3.3 Å3/Da / Density % sol: 62.7 %
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: ID14-1 / Wavelength: 0.934
DetectorDate: Jun 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.4→33 Å / Num. obs: 70856 / % possible obs: 98.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.1
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 3.2 / % possible all: 97.7
Reflection
*PLUS
Highest resolution: 1.4 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 97.7 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NAE

1nae


Resolution: 1.4→33.52 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.651 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.178 3577 5 %RANDOM
Rwork0.161 ---
obs0.162 67276 100 %-
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: 13.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.33 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.4→33.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1944 0 0 391 2335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211992
X-RAY DIFFRACTIONr_bond_other_d0.0020.021668
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.8872720
X-RAY DIFFRACTIONr_angle_other_deg0.74833892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4135260
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_restr0.0780.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022308
X-RAY DIFFRACTIONr_gen_planes_other0.010.02390
X-RAY DIFFRACTIONr_nbd_refined0.1790.2280
X-RAY DIFFRACTIONr_nbd_other0.2630.22020
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.21241
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2266
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3240.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8091.51276
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51122034
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1883716
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4184.5686
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: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.208 240
Rwork0.184 4877
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS

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