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- PDB-3a3h: CELLOTRIOSE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGAR... -

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Basic information

Entry
Database: PDB / ID: 3a3h
TitleCELLOTRIOSE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHERANS AT 1.6 A RESOLUTION
ComponentsENDOGLUCANASE
KeywordsHYDROLASE / CELLULOSE DEGRADATION / ENDOGLUCANASE / GLYCOSIDE HYDROLASE FAMILY 5
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
alpha-cellotriose / Endoglucanase 5A
Similarity search - Component
Biological speciesBacillus agaradhaerens (bacteria)
MethodX-RAY DIFFRACTION / ISOMORPHOUS WITH NATIVE STRUCTURE / Resolution: 1.64 Å
AuthorsDavies, G.J. / Brzozowski, A.M. / Andersen, K. / Schulein, M.
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
DepositionFeb 1, 1998Processing site: BNL
Revision 1.0Mar 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_validate_chiral / 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_atom_id / _atom_site.label_comp_id / _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.type / _pdbx_database_status.process_site / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)34,1582
Polymers33,6541
Non-polymers5041
Water7,170398
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.710, 69.570, 77.040
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: 33653.746 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE
Source method: isolated from a genetically manipulated source
Details: THIS IS A COMPLEX WITH B-D-CELLOTRIOSE BOUND IN THE -1, -2 AND -3 SITES OF THE ENZYME
Source: (gene. exp.) Bacillus agaradhaerens (bacteria) / Strain: AC13 / 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)-alpha-D-glucopyranose / alpha-cellotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE FIRST 3 RESIDUES ARE DISORDERED SO IT STARTS WITH RESIDUE SER 4. THIS THE NATURALLY OCCURRING ...THE FIRST 3 RESIDUES ARE DISORDERED SO IT STARTS WITH RESIDUE SER 4. THIS THE NATURALLY OCCURRING CATALYTIC CORE DOMAIN AFTER LOSS OF THE CELLULOSE-BINDING DOMAIN(S).

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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: 2.18 Å3/Da / Density % sol: 44 %
Crystal growpH: 4.5 / Details: pH 4.5
Crystal grow
*PLUS
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: May 1, 1997 / Details: LONG FOCUSSING MIRRORS (MSC)
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→20 Å / Num. obs: 19752 / % possible obs: 99.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 19.1
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 7.6 / Rsym value: 0.174 / % possible all: 98.8
Reflection
*PLUS
Lowest resolution: 15 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 97.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.184

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: ISOMORPHOUS WITH NATIVE STRUCTURE
Resolution: 1.64→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: ESTIMATED COORDINATE ERROR. ESD FROM SIGMAA (A) : 0.013 LOW RESOLUTION CUTOFF (A) : 15
RfactorNum. reflection% reflectionSelection details
Rfree0.176 1052 5 %RANDOM
Rwork0.148 ---
obs-19697 99 %-
Displacement parametersBiso mean: 12.6 Å2
Refine analyzeLuzzati d res low obs: 15 Å / Luzzati sigma a obs: 0.01 Å
Refinement stepCycle: LAST / Resolution: 1.64→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 34 398 2809
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.93
X-RAY DIFFRACTIONp_mcangle_it2.45
X-RAY DIFFRACTIONp_scbond_it3.44
X-RAY DIFFRACTIONp_scangle_it4.76
X-RAY DIFFRACTIONp_plane_restr0.010.04
X-RAY DIFFRACTIONp_chiral_restr0.130.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.2390.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1940.3
X-RAY DIFFRACTIONp_planar_tor4.57
X-RAY DIFFRACTIONp_staggered_tor13.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.920
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.148
Solvent computation
*PLUS
Displacement parameters
*PLUS

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