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- PDB-7a3h: NATIVE ENDOGLUCANASE CEL5A CATALYTIC CORE DOMAIN AT 0.95 ANGSTROM... -

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Basic information

Entry
Database: PDB / ID: 7a3h
TitleNATIVE ENDOGLUCANASE CEL5A CATALYTIC CORE DOMAIN AT 0.95 ANGSTROMS 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
ETHANOL / Endoglucanase 5A
Similarity search - Component
Biological speciesBacillus agaradhaerens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 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
DepositionAug 5, 1998Processing site: BNL
Revision 1.0Aug 6, 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 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDOGLUCANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1363
Polymers33,9981
Non-polymers1382
Water8,701483
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 / CEL5A / CELLULASE


Mass: 33998.023 Da / Num. of mol.: 1 / Fragment: CATALYTIC CORE DOMAIN
Source method: isolated from a genetically manipulated source
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS THE NATURALLY OCCURRING CATALYTIC CORE DOMAIN AFTER LOSS OF THE CELLULOSE-BINDING DOMAIN(S). ...THIS THE NATURALLY OCCURRING CATALYTIC CORE DOMAIN AFTER LOSS OF THE CELLULOSE-BINDING DOMAIN(S). CEL5A IS A MEMBER OF GLYCOSIDE HYDROLASE FAMILY 5. THIS IS ONE OF THE GH-A CLAN MEMBERS.

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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: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1997
RadiationMonochromator: YES / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 0.95→20 Å / Num. obs: 170547 / % possible obs: 97 % / Redundancy: 5 % / Biso Wilson estimate: 6.7 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 31
Reflection shellResolution: 0.95→0.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.3 / % possible all: 83.8
Reflection shell
*PLUS
% possible obs: 83.8 %

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Processing

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

1a3h


Resolution: 0.95→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE STRUCTURE WAS INITIALLY REFINED ANISOTROPICALLY WITH SHELXL-97. THIS REFINEMENT IS WITH A PRE-RELEASE VERSION OF REFMAC. THE AUTHORS WILL UPDATE THIS COORDINATE SET AS SOON AS BETTER ...Details: THE STRUCTURE WAS INITIALLY REFINED ANISOTROPICALLY WITH SHELXL-97. THIS REFINEMENT IS WITH A PRE-RELEASE VERSION OF REFMAC. THE AUTHORS WILL UPDATE THIS COORDINATE SET AS SOON AS BETTER REFINEMENT PROTOCOLS BECOME AVAILABLE.
RfactorNum. reflection% reflectionSelection details
Rfree0.13 8854 5 %RANDOM
Rwork0.11 ---
obs-176480 99.6 %-
Refinement stepCycle: LAST / Resolution: 0.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 9 483 2869
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0270.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.72
X-RAY DIFFRACTIONp_mcangle_it2.33
X-RAY DIFFRACTIONp_scbond_it2.72
X-RAY DIFFRACTIONp_scangle_it3.73
X-RAY DIFFRACTIONp_plane_restr0.0230.0125
X-RAY DIFFRACTIONp_chiral_restr0.1160.15
X-RAY DIFFRACTIONp_singtor_nbd0.1710.3
X-RAY DIFFRACTIONp_multtor_nbd0.2620.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.0910.3
X-RAY DIFFRACTIONp_planar_tor6.17
X-RAY DIFFRACTIONp_staggered_tor12.415
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: 0.11
Solvent computation
*PLUS
Displacement parameters
*PLUS

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