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- PDB-1dys: Endoglucanase CEL6B from Humicola insolens -

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Basic information

Entry
Database: PDB / ID: 1dys
TitleEndoglucanase CEL6B from Humicola insolens
ComponentsENDOGLUCANASE
KeywordsCELLULASE / HYDROLASE / CELLULOSE DEGRADATION / GLYCOSIDE HYDROLASE FAMILY 6
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process
Similarity search - Function
Glycosyl hydrolases family 6 signature 2. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesHUMICOLA INSOLENS (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDavies, G.J. / Brzozowski, A.M. / Dauter, M. / Varrot, A. / Schulein, M.
CitationJournal: Biochem.J. / Year: 2000
Title: Structure and Function of Humicola Insolens Family 6 Cellulases: Structure of the Endoglucanase, Cel6B, at 1.6 A Resolution
Authors: Davies, G.J. / Brzozowski, A.M. / Dauter, M. / Varrot, A. / Schulein, M.
History
DepositionFeb 8, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2001Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. EACH IS ... SHEET DETERMINATION METHOD: DSSP THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. EACH IS REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS A AND A1 REPRESENT ONE BIFURCATED SHEET. SHEETS C AND C1 REPRESENT ONE BIFURCATED SHEET.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDOGLUCANASE
B: ENDOGLUCANASE


Theoretical massNumber of molelcules
Total (without water)75,5722
Polymers75,5722
Non-polymers00
Water16,232901
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-7 kcal/mol
Surface area31780 Å2
MethodPQS
Unit cell
Length a, b, c (Å)109.917, 104.451, 53.788
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.162288, 0.986735, -0.004104), (0.985101, 0.162256, 0.057009), (0.056919, 0.005209, -0.998365)
Vector: 4.43538, -4.14676, 23.77936)
DetailsBIOLOGICAL_UNIT: ACTIVE AS A MONOMER

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Components

#1: Protein ENDOGLUCANASE / CELLULASE


Mass: 37785.832 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMICOLA INSOLENS (fungus) / Cellular location: EXCRETED / Production host: ASPERGILLUS ORYZAE (mold) / References: UniProt: Q7SIG5*PLUS, cellulase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 901 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREFERENCE: SEQUENCE NOT YET 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: 2.08 Å3/Da / Density % sol: 40.5 %
Crystal growpH: 7.5
Details: THE PROTEIN (20 MG/ML-1) WAS CRYSTALLISED FROM 30% (W/V) PEG 4000K IN 10MM TRIS-ACETATE BUFFER AT PH 7.5
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlprotein1drop
225 %(w/v)PEG40001reservoir
30.2 M1reservoirLi2SO4
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1997 / Details: LONG MIRRORS (MSC)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→15 Å / Num. obs: 78038 / % possible obs: 98.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 17
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 3.6 / % possible all: 97.8
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 15 Å
Reflection shell
*PLUS
Highest resolution: 1.6 Å / % possible obs: 98 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRICHODERMA REESEI CELLOBIOHYDROLASE II (T A JONES, PERSONAL COMMUNICATION)

Resolution: 1.6→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: TWO MOLECULES IN ASYMMETRIC UNIT RESIDUE ALA 182 LIES IN A FORBIDDEN REGION OF THE RAMACHANDRAN PLOT. IT IS PART OF A HYDROGEN-BONDING NETWROK IN THE ACTIVE- SITE AND IS NOT AN ERROR. THE ...Details: TWO MOLECULES IN ASYMMETRIC UNIT RESIDUE ALA 182 LIES IN A FORBIDDEN REGION OF THE RAMACHANDRAN PLOT. IT IS PART OF A HYDROGEN-BONDING NETWROK IN THE ACTIVE- SITE AND IS NOT AN ERROR. THE FIRST TWO RESIDUES ARE NOT VISIBLE IN THE ELECTRON DENSITY. THE STRUCTURE CONTAINS ONLY THE CATALYTIC CORE DOMAIN WHICH TERMINATES WITH RESIDUE ALA 347. THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.24 -5 %RANDOM
Rwork0.18 ---
obs-78038 98.9 %-
Displacement parametersBiso mean: 22 Å2
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5270 0 0 901 6171
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.93
X-RAY DIFFRACTIONp_mcangle_it3.55
X-RAY DIFFRACTIONp_scbond_it4.34
X-RAY DIFFRACTIONp_scangle_it5.26
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.120.15
X-RAY DIFFRACTIONp_singtor_nbd0.1740.3
X-RAY DIFFRACTIONp_multtor_nbd0.2520.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1650.3
X-RAY DIFFRACTIONp_planar_tor4.27
X-RAY DIFFRACTIONp_staggered_tor16.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor33.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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