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- PDB-4a3h: 2',4' DINITROPHENYL-2-DEOXY-2-FLURO-B-D-CELLOBIOSIDE COMPLEX OF T... -

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Basic information

Entry
Database: PDB / ID: 4a3h
Title2',4' DINITROPHENYL-2-DEOXY-2-FLURO-B-D-CELLOBIOSIDE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS AT 1.6 A RESOLUTION
ComponentsPROTEIN (ENDOGLUCANASE)
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
Chem-DCB / Endoglucanase 5A / Endoglucanase B
Similarity search - Component
Biological speciesBacillus agaradhaerens (bacteria)
MethodX-RAY DIFFRACTION / ISOMORPHOUS WITH NATIVE STRUCTURE / Resolution: 1.65 Å
AuthorsDavies, G.J. / Brzozowski, A.M. / Andersen, K. / 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, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 23, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ENDOGLUCANASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5082
Polymers33,9981
Non-polymers5101
Water7,512417
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 PROTEIN (ENDOGLUCANASE) / E.C.3.2.1.4 HYDROLASE / 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 2,4-DINITROPHENYL, 2-FLUOROCELLOBIOSEOUND IN THE -1, -2 AND +1 SITES OF THE ENZYME
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: P06565, UniProt: O85465*PLUS, cellulase
#2: Chemical ChemComp-DCB / 2,4-DINITROPHENYL-2-DEOXY-2-FLUORO-BETA-D-CELLOBIOSIDE / 2',4'-DINITROPHENYL-2DEOXY-2-FLURO-B-D-CELLOBIOSIDE


Mass: 510.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H23FN2O14
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCEL5A IS A MEMBER OF GLYCOSIDE HYDROLASE FAMILY 5 THIS IS ONE OF THE GH-A CLAN MEMBERS
Nonpolymer detailsHET ID DCB THE CELLOBIOSE MOEITY IS BOUND IN THE -2 AND -1 SUBSITES WITH THE UNHYDROLYSED DNP GROUP IN +1.
Sequence detailsREFERENCE: SEQUENCE NOT DEPOSITED.

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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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growpH: 5.5
Details: PROTEIN (20MGML-1) WAS CRYSTALLISED FROM 1.0M AMMONIUM SULPHATE AS BOTH BUFFER AND PRECIPITANT AT PH 4.5 IN THE PRESENCE OF 15% (W/V) GLYCEROL, pH 5.5 THIS STRUCTURE WAS OBTAINED BY SOAKING ...Details: PROTEIN (20MGML-1) WAS CRYSTALLISED FROM 1.0M AMMONIUM SULPHATE AS BOTH BUFFER AND PRECIPITANT AT PH 4.5 IN THE PRESENCE OF 15% (W/V) GLYCEROL, pH 5.5 THIS STRUCTURE WAS OBTAINED BY SOAKING THE CRYSTALS IN 10MM 2",4" DINITROPHENYL-2-DEOXY-2-FLUORO-B-D-CELLOBIOSIDE FOR 12 H PRIOR TO DATA COLLECTION.
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 RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1997 / Details: LONG FOCUSSING MIRRORS (MSC)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 35964 / % possible obs: 99.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 22.6
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 13.4 / Rsym value: 0.176 / % possible all: 99.9
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: ISOMORPHOUS WITH NATIVE STRUCTURE
Resolution: 1.65→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.172 1832 5 %RANDOM
Rwork0.142 ---
obs-35910 99.9 %-
Displacement parametersBiso mean: 15.8 Å2
Refinement stepCycle: LAST / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 35 417 2829
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.63
X-RAY DIFFRACTIONp_mcangle_it2.15
X-RAY DIFFRACTIONp_scbond_it3.14
X-RAY DIFFRACTIONp_scangle_it4.56
X-RAY DIFFRACTIONp_plane_restr0.0120.04
X-RAY DIFFRACTIONp_chiral_restr0.130.11
X-RAY DIFFRACTIONp_singtor_nbd0.1740.3
X-RAY DIFFRACTIONp_multtor_nbd0.2450.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1690.3
X-RAY DIFFRACTIONp_planar_tor4.57
X-RAY DIFFRACTIONp_staggered_tor13.215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.14
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_chiral_restr0.11
X-RAY DIFFRACTIONp_mcbond_it1.6
X-RAY DIFFRACTIONp_scbond_it3.1
X-RAY DIFFRACTIONp_mcangle_it2.1
X-RAY DIFFRACTIONp_scangle_it4.5

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