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- PDB-1up2: Structure of the endoglucanase Cel6 from Mycobacterium tuberculos... -

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Basic information

Entry
Database: PDB / ID: 1up2
TitleStructure of the endoglucanase Cel6 from Mycobacterium tuberculosis in complex with glucose-isofagomine at 1.9 angstrom
ComponentsCELA1 PROTEIN
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / FAMILY 6
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulase activity / cellulose catabolic process / extracellular region / membrane
Similarity search - Function
1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / 1, 4-beta cellobiohydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-1PG / ACETATE ION / beta-D-glucopyranose / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Glucanase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVarrot, A. / Leydier, S. / Pell, G. / Gilbert, H.J. / Davies, G.J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Mycobacterium Tuberculosis Strains Possess Functional Cellulases.
Authors: Varrot, A. / Leydier, S. / Pell, G. / Macdonald, J.M. / Stick, R.V. / Henrissat, B. / Gilbert, H.J. / Davies, G.J.
History
DepositionSep 26, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_special_symmetry / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3May 1, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CELA1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,80010
Polymers30,5831
Non-polymers1,2179
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.788, 92.830, 46.695
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2110-

HOH

21A-2147-

HOH

31A-2252-

HOH

41A-2255-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein CELA1 PROTEIN / ENDOGLUCANASE / CELA / CEL6


Mass: 30582.652 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 88-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Description: SYNTHETIC GENE / Plasmid: PET22B / Production host: ESCHERICHIA COLI BL21 (bacteria) / Variant (production host): ORIGAMI / References: UniProt: Q79G13
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 414 molecules

#2: Chemical ChemComp-IFM / 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE / Afegostat / isofagomine / (3R,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-3,4-DIOL


Mass: 147.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsONLY THE CATALYTIC DOMAIN HAS BEEN CLONED CORRESPONDING TO RESIDUES 88 TO 380.

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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: 2.03 Å3/Da / Density % sol: 38.81 %
Crystal growpH: 4.6
Details: 12 % PEG 4K, 12 % PEG 4K, 100 MM SODIUM ACTETATE PH 4.6, 200 MM LISO4. THE PROTEIN WAS AT 10MG/ML AND INCUBATED WITH 1 MM OF GLUCOSE-ISOFAGOMINE FOR 1 HOUR PRIOR CRYSTALLISATION. 30% PEG 400 ...Details: 12 % PEG 4K, 12 % PEG 4K, 100 MM SODIUM ACTETATE PH 4.6, 200 MM LISO4. THE PROTEIN WAS AT 10MG/ML AND INCUBATED WITH 1 MM OF GLUCOSE-ISOFAGOMINE FOR 1 HOUR PRIOR CRYSTALLISATION. 30% PEG 400 ADDED AS CRYOPROTECTANT

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 2003 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 21248 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 14.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 4.9 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: COMPLEX WITH SDP5

Resolution: 1.9→19.8 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.54 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.177 1079 5.1 %RANDOM
Rwork0.132 ---
obs0.134 20168 97.8 %-
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: 11.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2145 0 70 407 2622
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212288
X-RAY DIFFRACTIONr_bond_other_d0.0020.021985
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9733137
X-RAY DIFFRACTIONr_angle_other_deg1.0634599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5465297
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_restr0.0970.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022618
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02462
X-RAY DIFFRACTIONr_nbd_refined0.2210.2512
X-RAY DIFFRACTIONr_nbd_other0.2570.22327
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.21176
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2254
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0930.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6961.51477
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16422337
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1033811
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3464.5798
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.219 81
Rwork0.17 1373

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