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- PDB-6a3h: 2-DEOXY-2-FLURO-B-D-CELLOTRIOSYL/ENZYME INTERMEDIATE COMPLEX OF T... -

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Basic information

Entry
Database: PDB / ID: 6a3h
Title2-DEOXY-2-FLURO-B-D-CELLOTRIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.6 ANGSTROM RESOLUTION
ComponentsENDOGLUCANASE
KeywordsHYDROLASE / CELLULOSE DEGRADATION / ENDOGLUCANASE / GLYCOSIDE HYDROLASE FAMILY 5 / MICHAELIS COMPLEX / SKEW-BOAT / DISTORTION
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 / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsDavies, G.J. / Varrot, A. / Dauter, M. / Brzozowski, A.M. / Schulein, M. / Mackenzie, L. / Withers, S.G.
Citation
Journal: Biochemistry / Year: 1998
Title: Snapshots along an enzymatic reaction coordinate: analysis of a retaining beta-glycoside hydrolase.
Authors: Davies, G.J. / Mackenzie, L. / Varrot, A. / Dauter, M. / Brzozowski, A.M. / Schulein, M. / Withers, S.G.
#1: Journal: Biochemistry / Year: 1998
Title: Structure of the Bacillus Agaradherans Family 5 Endoglucanase at 1.6 A and its Cellobiose Complex at 2.0 A Resolution
Authors: Davies, G.J. / Dauter, M. / Brzozowski, A.M. / Bjornvad, M.E. / Andersen, K.V. / Schulein, M.
History
DepositionJul 22, 1998Processing site: BNL
Revision 1.0Jul 24, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / _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.process_site
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,24110
Polymers33,9981
Non-polymers1,2439
Water5,963331
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.280, 69.700, 76.940
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 / CELLULASE


Mass: 33998.023 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN ONLY
Source method: isolated from a genetically manipulated source
Details: THIS IS A COMPLEX WITH 2-DEOXY-2-FLUOROCELLOTRIOSE COVALENTLY LINKED TO THE ENZYMATIC NUCLEOPHILE, GLU 228
Source: (gene. exp.) Bacillus agaradhaerens (bacteria) / Strain: AC13 (NCIMB 40482) / Plasmid: THERMAMYL-AMYLASE PROMOTER SYSTEM / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCEL5A IS A MEMBER OF GLYCOSIDE HYDROLASE FAMILY 5, IT IS ONE OF THE GH-A CLAN MEMBERS. THIS ENTRY ...CEL5A IS A MEMBER OF GLYCOSIDE HYDROLASE FAMILY 5, IT IS ONE OF THE GH-A CLAN MEMBERS. THIS ENTRY REPRESENTS THE NATURALLY OCCURRING CATALYTIC CORE DOMAIN AFTER LOSS OF THE CELLULOSE-BINDING DOMAIN(S).
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 36.4 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion, hanging drop / Details: Davies, G.J., (1998) Biochemistry, 37, 1926.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.8-1.2 Mammonium sulfate1reservoir
215 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997 / Details: YALE/MSC MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→15 Å / Num. obs: 34744 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 13.47 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 23.9
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 4.6 / Rsym value: 0.317 / % possible all: 98.3
Reflection shell
*PLUS
% possible obs: 98.3 %

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A3H

1a3h


Resolution: 1.68→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1747 5 %RANDOM
Rwork0.15 ---
obs-34342 99.5 %-
Displacement parametersBiso mean: 15.3 Å2
Refinement stepCycle: LAST / Resolution: 1.68→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 81 331 2789
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.0220.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0230.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.2133
X-RAY DIFFRACTIONp_mcangle_it1.7675
X-RAY DIFFRACTIONp_scbond_it2.1274
X-RAY DIFFRACTIONp_scangle_it3.0996
X-RAY DIFFRACTIONp_plane_restr0.020.03
X-RAY DIFFRACTIONp_chiral_restr0.1070.15
X-RAY DIFFRACTIONp_singtor_nbd0.1740.3
X-RAY DIFFRACTIONp_multtor_nbd0.2320.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1160.3
X-RAY DIFFRACTIONp_planar_tor3.67
X-RAY DIFFRACTIONp_staggered_tor12.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor2920
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.15 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS

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