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- PDB-1cgv: SITE DIRECTED MUTATIONS OF THE ACTIVE SITE RESIDUE TYROSINE 195 O... -

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Basic information

Entry
Database: PDB / ID: 1cgv
TitleSITE DIRECTED MUTATIONS OF THE ACTIVE SITE RESIDUE TYROSINE 195 OF CYCLODEXTRIN GLYCOSYLTRANSFERASE FROM BACILLUS CIRCULANS STRAIN 251 AFFECTING ACTIVITY AND PRODUCT SPECIFICITY
ComponentsCYCLOMALTODEXTRIN GLUCANOTRANSFERASE
KeywordsGLYCOSYLTRANSFERASE
Function / homology
Function and homology information


cyclomaltodextrin glucanotransferase / cyclomaltodextrin glucanotransferase activity / starch binding / alpha-amylase activity / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function
Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase ...Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase / IPT/TIG domain / IPT domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Cyclomaltodextrin glucanotransferase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsStrokopytov, B.V. / Dijkstra, B.W.
Citation
Journal: Biochemistry / Year: 1995
Title: Site-directed mutations in tyrosine 195 of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 affect activity and product specificity.
Authors: Penninga, D. / Strokopytov, B. / Rozeboom, H.J. / Lawson, C.L. / Dijkstra, B.W. / Bergsma, J. / Dijkhuizen, L.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Nucleotide Sequence and X-Ray Structure of Cyclodextrin Glycosyltransferase from Bacillus Circulans Strain 251 in a Maltose-Dependent Crystal Form
Authors: Lawson, C.L.L. / Van Montfort, R. / Strokopytov, B. / Rozeboom, H.J. / Kalk, K.H. / De Vries, G.E. / Penninga, D. / Dijkhuizen, L. / Dijkstra, B.W.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Maltodextrin-Dependent Crystallization of Cyclomaltodextrin Glucanotransferase from Bacillus Circulans
Authors: Lawson, C.L.L. / Bergsma, J. / Bruinenberg, P.M. / De Vries, G.E. / Dijkhuizen, L. / Dijkstra, B.W.
History
DepositionAug 5, 1994Processing site: BNL
Revision 1.0Feb 27, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 7, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_ref_seq_dif.details
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: CYCLOMALTODEXTRIN GLUCANOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6676
Polymers74,5591
Non-polymers1,1075
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.031, 111.107, 66.302
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 372 / 2: CIS PROLINE - PRO 506 / 3: CIS PROLINE - PRO 624 / 4: CIS PROLINE - PRO 634

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Components

#1: Protein CYCLOMALTODEXTRIN GLUCANOTRANSFERASE


Mass: 74559.484 Da / Num. of mol.: 1 / Mutation: Y195F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria)
References: UniProt: P43379, cyclomaltodextrin glucanotransferase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.84 %
Crystal grow
*PLUS
Method: vapor diffusion

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 29 Å / Num. obs: 28296 / % possible obs: 87.3 % / Num. measured all: 84161 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.58 Å / % possible obs: 45 %

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.5→20 Å / σ(F): 0 /
RfactorNum. reflection
obs0.155 28252
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5263 0 71 171 5505
Refinement
*PLUS
Highest resolution: 2.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONt_bond_d0.010.8
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.11.3
X-RAY DIFFRACTIONt_dihedral_angle_d17.430
X-RAY DIFFRACTIONt_plane_restr0.0125

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