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- PDB-4uz8: The SeMet structure of the family 46 carbohydrate-binding module ... -

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Basic information

Entry
Database: PDB / ID: 4uz8
TitleThe SeMet structure of the family 46 carbohydrate-binding module (CBM46) of endo-beta-1,4-glucanase B (Cel5B) from Bacillus halodurans
ComponentsENDO-BETA-1,4-GLUCANASE (CELULASE B)
KeywordsSUGAR BINDING PROTEIN / CARBOHYDRATE BINDING PROTEIN / CARBOHYDRATE-BINDING MODULE FAMILY 46 / CBM46 / CEL5B / BACILLUS HALODURANS / SEMET DERIVATIVE
Function / homology
Function and homology information


beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region / metal ion binding
Similarity search - Function
Endoglucanase B, carbohydrate binding domain / Carbohydrate binding domain / Glycoside hydrolase, family 5, endoglucanase B / Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / : / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Endo-beta-1,4-glucanase (Celulase B)
Similarity search - Component
Biological speciesBACILLUS HALODURANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsVenditto, I. / Santos, H. / Ferreira, L.M.A. / Sakka, K. / Fontes, C.M.G.A. / Najmudin, S.
Citation
Journal: J.Biol.Chem. / Year: 2015
Title: Family 46 Carbohydrate-Binding Modules Contribute to the Enzymatic Hydrolysis of Xyloglucan and Beta-1,3-1,4-Glucans Through Distinct Mechanisms.
Authors: Venditto, I. / Najmudin, S. / Luis, A.S. / Ferreira, L.M. / Sakka, K. / Knox, J.P. / Gilbert, H.J. / Fontes, C.M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Overproduction, Purification, Crystallization and Preliminary X-Ray Characterization of the Family 46 Carbohydrate-Binding Module (Cbm46) of Endo-Beta-1,4-Glucanase B (Celb) from Bacillus Halodurans
Authors: Venditto, I. / Santos, H. / Ferreira, L.M.A. / Sakka, K. / Fontes, C.M.G.A. / Najmudin, S.
History
DepositionSep 4, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDO-BETA-1,4-GLUCANASE (CELULASE B)
B: ENDO-BETA-1,4-GLUCANASE (CELULASE B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1253
Polymers29,0292
Non-polymers961
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.850, 120.850, 76.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-2009-

HOH

21A-2027-

HOH

31B-2002-

HOH

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Components

#1: Protein ENDO-BETA-1,4-GLUCANASE (CELULASE B)


Mass: 14514.273 Da / Num. of mol.: 2
Fragment: CARBOHYDRATE BINDING MODULE FAMILY 46, UNP RESIDUES 457-563
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONYLATED DERIVATIVE / Source: (gene. exp.) BACILLUS HALODURANS (bacteria) / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: Q9KF82
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsSULFATE ION (SO4): FROM CRYSTALLISATION BUFFER

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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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 7
Details: 0.2 M AMMONIUM SULFATE, 30% W/V POLYETHYLENE GLYCOL 4,000, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97976 Å / Relative weight: 1
ReflectionResolution: 2.3→85.45 Å / Num. obs: 12870 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 19.1 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
FAST_DPdata scaling
PHENIXAUTOSOLphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→85.45 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 17.115 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. THE COORDINATE FILE WA REFINED BY PDB_REDO IN THE PENULTIMATE ROOUND OF REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.25449 629 4.9 %RANDOM
Rwork0.20388 ---
obs0.20639 12230 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.834 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.3→85.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 5 59 1726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191741
X-RAY DIFFRACTIONr_bond_other_d0.0050.021541
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.922372
X-RAY DIFFRACTIONr_angle_other_deg1.21233534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.6515219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47324.17691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.66815242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.522159
X-RAY DIFFRACTIONr_chiral_restr0.1190.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022066
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02459
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5271.945858
X-RAY DIFFRACTIONr_mcbond_other3.5271.946857
X-RAY DIFFRACTIONr_mcangle_it4.9312.9021071
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.1792.354875
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 54 -
Rwork0.266 857 -
obs--99.35 %
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)
16.29530.53632.37923.51661.06564.7187-0.6871.27990.4906-0.28070.2024-0.0781-0.6450.71620.48450.2053-0.2153-0.17120.39070.15270.1821-15.650.349-20.02
24.69092.7306-0.236911.1611-0.9181.3014-0.610.2725-0.6741-2.06750.2557-0.34640.4204-0.00640.35430.5675-0.00570.17360.0339-0.02460.1887-1.405-19.04-10.573
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A457 - 563
2X-RAY DIFFRACTION2B458 - 563

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