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- PDB-1h11: 2-DEOXY-2-FLURO-B-D-CELLOTRIOSYL/ENZYME INTERMEDIATE COMPLEX OF T... -

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Basic information

Entry
Database: PDB / ID: 1h11
Title2-DEOXY-2-FLURO-B-D-CELLOTRIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.08 ANGSTROM RESOLUTION
ComponentsENDOGLUCANASE 5A
KeywordsHYDROLASE / CELLULOSE DEGRADATION / GLYCOSIDASE / ENDOGLUCANASE
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
2-deoxy-2-fluoro-beta-cellotriose / Endoglucanase 5A
Similarity search - Component
Biological speciesBACILLUS AGARADHAERENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.08 Å
AuthorsVarrot, A. / Davies, G.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Direct Experimental Observation of the Hydrogen-Bonding Network of a Glycosidase Along its Reaction Coordinate Revealed by Atomic Resolution Analyses of Endoglucanase Cel5A
Authors: Varrot, A. / Davies, G.J.
History
SupersessionJul 1, 2002ID: 1HF5
DepositionJul 1, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification
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)34,7855
Polymers33,9981
Non-polymers7874
Water9,188510
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.447, 69.880, 77.322
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 33998.023 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN ONLY, RESIDUES 27-329
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: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-2-deoxy-2-fluoro-alpha-D-glucopyranose / 2-deoxy-2-fluoro-beta-cellotriose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 506.429 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2-deoxy-2-fluoro-beta-cellotriose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5_2*F][a2122h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp2fluoro]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 510 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FIRST 26 RESIDUES IN THE DATABASE CORRESPOND TO THE PROSEQUENCE. OUR NUMBERING BEGIN AT THE ...THE FIRST 26 RESIDUES IN THE DATABASE CORRESPOND TO THE PROSEQUENCE. OUR NUMBERING BEGIN 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: 1.9 Å3/Da / Density % sol: 35.58 % / Description: STARTING MODEL: PDB ENTRY 6A3H
Crystal growpH: 5.5
Details: PROTEIN CONCENTRATION 20MG/ML, 2M AMMONIUM SULPHATE, 25% GLYCEROL AS CRYOPROTECTANT, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.08→20 Å / Num. obs: 540161 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 22
Reflection shellResolution: 1.08→1.12 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 5 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: OTHER / Resolution: 1.08→20 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.273 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.125 6334 5 %RANDOM
Rwork0.108 ---
obs0.109 119386 99.2 %-
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: 9.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2---0.75 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 1.08→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 50 510 2937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212607
X-RAY DIFFRACTIONr_bond_other_d0.0010.022184
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.9121.9413567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg2.08735136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr6.3735309
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022899
X-RAY DIFFRACTIONr_gen_planes_other0.010.02496
X-RAY DIFFRACTIONr_nbd_refined0.2190.2529
X-RAY DIFFRACTIONr_nbd_other0.2690.22512
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.21280
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3120.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.234
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3821.51533
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9922499
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.59531074
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6954.51066
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: 1.08→1.11 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.172 460
Rwork0.153 8108

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