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- PDB-1w3k: ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN COMPLEX WITH C... -

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Basic information

Entry
Database: PDB / ID: 1w3k
TitleENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN COMPLEX WITH CELLOBIO DERIVED-TETRAHYDROOXAZINE
ComponentsENDOGLUCANASE 5A
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / CELLULOSE DEGRADATION / ENDOGLUCANASE / FAMILY 5 / TETRAHYDROOXAZINE
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process / carbohydrate binding / extracellular region
Similarity search - Function
Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily ...Carbohydrate-binding module family 5/12 / Chitin-binding domain type 3 / Carbohydrate-binding module family 5/12 / Carbohydrate-binding module superfamily 5/12 / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / TETRAHYDROOXAZINE / Endoglucanase 5A
Similarity search - Component
Biological speciesBACILLUS AGARADHAERENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsGloster, T.M. / Macdonald, J.M. / Tarling, C.A. / Stick, R.V. / Withers, S.W. / Davies, G.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural, Thermodynamic, and Kinetic Analyses of Tetrahydrooxazine-Derived Inhibitors Bound to {Beta}-Glucosidases
Authors: Gloster, T.M. / Macdonald, J.M. / Tarling, C.A. / Stick, R.V. / Withers, S.W. / Davies, G.J.
History
DepositionJul 16, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 8, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 2023Group: 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOGLUCANASE 5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6086
Polymers33,9981
Non-polymers6105
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)54.565, 69.559, 76.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein ENDOGLUCANASE 5A / ENDO-1 / 4-BETA-GLUCANASE / ALKALINE CELLULASE


Mass: 33998.023 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN, RESIDUES 30-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS AGARADHAERENS (bacteria) / Plasmid: THERMAMYL-AMYLASE PROMOT / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): PL2306 / References: UniProt: O85465, cellulase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
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 , 4 types, 464 molecules

#3: Chemical ChemComp-OXZ / TETRAHYDROOXAZINE


Mass: 149.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE FIRST 26 RESIDUES IN THE DATABASE CORRESPOND TO THE PROSEQUENCE. OUR NUMBERING BEGINS AT THE ...THE FIRST 26 RESIDUES IN THE DATABASE CORRESPOND TO THE PROSEQUENCE. OUR NUMBERING BEGINS AT THE FIRST RESIDUE OBTAINED AFTER CLEAVAGE OF THE PROSEQUENCE

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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: 2.1 Å3/Da / Density % sol: 42 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL
Crystal growpH: 5
Details: PROTEIN CONCENTRATION 20MG/ML, 1.3 M AMMONIUM SULPHATE PH 5.0, 25% GLYCEROL AS CRYOPROTECTANT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 2003 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 85611 / % possible obs: 98.1 % / Redundancy: 3.92 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 25.5
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 3.23 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.93 / % possible all: 89.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OCQ

1ocq


Resolution: 1.2→51.3 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.982 / SU B: 1.024 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.132 4520 5 %RANDOM
Rwork0.113 ---
obs0.114 85611 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å20 Å2
2---0.83 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.2→51.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 38 460 2875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222601
X-RAY DIFFRACTIONr_bond_other_d0.0020.022221
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9353550
X-RAY DIFFRACTIONr_angle_other_deg0.96335211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3155306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16725.804143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.02515418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.042159
X-RAY DIFFRACTIONr_chiral_restr0.0990.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022901
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02501
X-RAY DIFFRACTIONr_nbd_refined0.2090.2544
X-RAY DIFFRACTIONr_nbd_other0.1880.22352
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21316
X-RAY DIFFRACTIONr_nbtor_other0.0870.21386
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2290
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0090.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2680.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4821.51970
X-RAY DIFFRACTIONr_mcbond_other0.541625
X-RAY DIFFRACTIONr_mcangle_it1.80822501
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.69131276
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6784.51049
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: 1.2→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 283 -
Rwork0.202 5606 -
obs--87.88 %

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