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- PDB-1hgy: CEL6A D221A mutant -

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Basic information

Entry
Database: PDB / ID: 1hgy
TitleCEL6A D221A mutant
ComponentsCELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II)
KeywordsHYDROLASE (O-GLYCOSYL) / GLYCOSIDASE / GLYCOPROTEIN
Function / homology
Function and homology information


cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose binding / cellulose catabolic process / extracellular region / identical protein binding
Similarity search - Function
Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / 1, 4-beta cellobiohydrolase / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily ...Glycosyl hydrolases family 6 signature 2. / Glycosyl hydrolases family 6 signature 1. / Glycoside hydrolase, family 6, conserved site / 1, 4-beta cellobiohydrolase / 1, 4-beta cellobiohydrolase superfamily / Glycosyl hydrolases family 6 / 1, 4-beta cellobiohydrolase / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-D-mannopyranose / alpha-D-glucopyranose / alpha-D-mannopyranose / Exoglucanase 2
Similarity search - Component
Biological speciesTRICHODERMA REESEI (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZou, J.-Y. / Kleywegt, G.J. / Jones, T.A.
Citation
Journal: J.Am.Chem.Soc. / Year: 2002
Title: The Active Site of Cellobiohydrolase Cel6A from Trichoderma Reesei: The Roles of Aspartic Acids D221 and D175
Authors: Koivula, A. / Ruohonen, L. / Wohlfahrt, G. / Reinikainen, T. / Teeri, T.T. / Piens, K. / Claeyssens, M. / Weber, M. / Vasella, A. / Becker, D. / Sinnott, M.L. / Zou, J.-Y. / Kleywegt, G.J. / ...Authors: Koivula, A. / Ruohonen, L. / Wohlfahrt, G. / Reinikainen, T. / Teeri, T.T. / Piens, K. / Claeyssens, M. / Weber, M. / Vasella, A. / Becker, D. / Sinnott, M.L. / Zou, J.-Y. / Kleywegt, G.J. / Szardenings, M. / Stahlberg, J. / Jones, T.A.
#1: Journal: Science / Year: 1990
Title: Three-Dimensional Structure of Cellobiohydrolase II from Trichoderma Reesei
Authors: Rouvinen, J. / Bergfors, T. / Teeri, T. / Knowles, J.K. / Jones, T.A.
History
DepositionDec 15, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II)
B: CELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,79022
Polymers78,0232
Non-polymers3,76720
Water3,333185
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A: CELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,07512
Polymers39,0111
Non-polymers2,06411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,71510
Polymers39,0111
Non-polymers1,7049
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.600, 67.500, 53.800
Angle α, β, γ (deg.)76.30, 75.20, 78.40
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999982, -0.004826, 0.003536), (-0.004027, 0.105745, -0.994385), (0.004425, -0.994382, -0.105762)
Vector: 33.088, 35.155, 22.255)

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Components

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Protein / Non-polymers , 2 types, 187 molecules AB

#1: Protein CELLOBIOHYDROLASE CEL6A (FORMERLY CALLED CBH II) / CEL6A (D221A)


Mass: 39011.285 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 83-447 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRICHODERMA REESEI (fungus) / Gene: CBH2 (D221A) / Gene (production host): CBH2 (D221A) / Production host: TRICHODERMA REESEI (fungus)
References: UniProt: P07987, cellulose 1,4-beta-cellobiosidase (non-reducing end)
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 20 molecules

#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-MAN / alpha-D-mannopyranose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-BMA / beta-D-mannopyranose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-GLC / alpha-D-glucopyranose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Compound detailsCHAIN A, B ENGINEERED MUTATION ASP 221 ALA. HYDROLYSIS OF 1,4-BETA-D-GLUCOSIDIC LINKAGES IN ...CHAIN A, B ENGINEERED MUTATION ASP 221 ALA. HYDROLYSIS OF 1,4-BETA-D-GLUCOSIDIC LINKAGES IN CELLULOSE AND CELLOTETRAOSE,

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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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growpH: 6 / Details: 20% PEG6000, 10MM MES BUFFER., pH 6.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Bergfors, T., (1989) J.Mol.Biol, 209, 167.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 %mPEG50001reservoir
220 mMMES1reservoirpH6.0
310 mM1reservoirCoCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.13→8 Å / Num. obs: 31767 / % possible obs: 80.3 % / Redundancy: 2.3 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.8
Reflection shellResolution: 2.13→2.29 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 1.9 / % possible all: 48.1
Reflection
*PLUS
Lowest resolution: 8 Å / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 48.1 %

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Processing

Software
NameVersionClassification
CNS1refinement
MADNESSdata reduction
MADNESSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WILDTYPE CEL6A

Resolution: 2.2→19.9 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 88331.74 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED THE CATALYTIC CORE STARTS AT RESIDUE 83.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1893 7.1 %RANDOM
Rwork0.198 ---
obs0.198 26776 81.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40 Å2 / ksol: 0.315808 e/Å3
Displacement parametersBiso mean: 22.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.22 Å2-5.1 Å2
2--0.08 Å20.48 Å2
3----0.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5488 0 234 185 5907
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.592.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.318 243 7.5 %
Rwork0.26 3008 -
obs--58.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PAR.GLYCOTOP.GLYCO
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
LS refinement shell
*PLUS
Rfactor Rwork: 0.26 / Rfactor obs: 0.26

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