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- PDB-1up3: Structure of the endoglucanase Cel6 from Mycobacterium tuberculos... -

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Basic information

Entry
Database: PDB / ID: 1up3
TitleStructure of the endoglucanase Cel6 from Mycobacterium tuberculosis in complex with METHYL-CELLOBIOSYL-4-DEOXY-4-THIO-BETA-D-CELLOBIOSIDE at 1.6 angstrom
ComponentsPUTATIVE CELLULASE CEL6
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 / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-1PG / : / Glucanase
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE CELLULASE CEL6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5459
Polymers30,5511
Non-polymers1,9948
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.893, 93.058, 46.690
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-2093-

HOH

21A-2128-

HOH

31A-2204-

HOH

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Components

#1: Protein PUTATIVE CELLULASE CEL6 / ENDOGLUCANASE / CELA


Mass: 30550.652 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 (E. coli) / Strain (production host): ORIGAMI / References: UniProt: O53607, UniProt: Q79G13*PLUS
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl beta- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-methyl beta-D-glucopyranoside


Type: oligosaccharide / Mass: 696.669 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[a2122h-1b_1-5_1*OC][a2122h-1b_1-5]/1-2-2-2/a4-b1_b4-c1*S*_c4-d1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Glcp]{[(4+1)][b-D-Glcp4SH]{[(4+S)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H24O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 39.06 %
Crystal growpH: 6.5
Details: 14 % PEG 4K, 100 MM MES 6.5, 200 MM LISO4. THE PROTEIN WAS AT 10MG/ML AND INCUBATED WITH 1 MM OF LIGAND FOR 1 HOUR PRIOR CRYSTALLISATION. 30 % PEG 400 WAS ADDED AS CRYOPROTECTANT, pH 6.50

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 35625 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 3 / % possible all: 95.6

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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: 1.6→19.84 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.321 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.174 1785 5 %RANDOM
Rwork0.138 ---
obs0.14 33839 98.2 %-
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: 9.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2143 0 102 327 2572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212334
X-RAY DIFFRACTIONr_bond_other_d0.0040.022036
X-RAY DIFFRACTIONr_angle_refined_deg1.571.9773190
X-RAY DIFFRACTIONr_angle_other_deg1.71234734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.495300
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_restr0.0950.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022628
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02469
X-RAY DIFFRACTIONr_nbd_refined0.2190.2506
X-RAY DIFFRACTIONr_nbd_other0.2560.22395
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.21207
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2177
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8891.51476
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57822351
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6283858
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2844.5835
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 122
Rwork0.192 2208

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