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- PDB-6cgt: HOXA COMPLEX OF CYCLODEXTRIN GLYCOSYLTRANSFERASE MUTANT -

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Basic information

Entry
Database: PDB / ID: 6cgt
TitleHOXA COMPLEX OF CYCLODEXTRIN GLYCOSYLTRANSFERASE MUTANT
ComponentsCYCLODEXTRIN GLYCOSYLTRANSFERASE
KeywordsGLYCOSYLTRANSFERASE / STARCH DEGRADATION / CYCLODEXTRIN
Function / homology
Function and homology information


cyclomaltodextrin glucanotransferase activity / cyclomaltodextrin glucanotransferase / starch binding / alpha-amylase activity / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function
Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate binding module family 20 / Carbohydrate-binding-like fold / Aamy_C / Alpha-amylase, C-terminal domain / Alpha amylase, C-terminal all-beta domain / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase ...Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate binding module family 20 / Carbohydrate-binding-like fold / Aamy_C / Alpha-amylase, C-terminal domain / Alpha amylase, C-terminal all-beta domain / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase / IPT/TIG domain / IPT domain / Alpha amylase, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, family 13, catalytic domain / Golgi alpha-mannosidase II / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / Immunoglobulin-like fold / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
OXIRANPSEUDOGLUCOSE / Cyclomaltodextrin glucanotransferase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / X-PLOR WITH WILD-TYPE MODEL / Resolution: 2.6 Å
AuthorsParsiegla, G. / Schulz, G.E.
Citation
Journal: Eur.J.Biochem. / Year: 1998
Title: Substrate binding to a cyclodextrin glycosyltransferase and mutations increasing the gamma-cyclodextrin production.
Authors: Parsiegla, G. / Schmidt, A.K. / Schulz, G.E.
#1: Journal: Biochemistry / Year: 1998
Title: Structure of Cyclodextrin Glycosyltransferase Complexed with a Derivative of its Main Product Beta-Cyclodextrin
Authors: Schmidt, A.K. / Cottaz, S. / Driguez, H. / Schulz, G.E.
#2: Journal: Biochemistry / Year: 1992
Title: Catalytic Center of Cyclodextrin Glycosyltransferase Derived from X-Ray Structure Analysis Combined with Site-Directed Mutagenesis
Authors: Klein, C. / Hollender, J. / Bender, H. / Schulz, G.E.
#3: Journal: J.Mol.Biol. / Year: 1991
Title: Structure of Cyclodextrin Glycosyltransferase Refined at 2.0 A Resolution
Authors: Klein, C. / Schulz, G.E.
#4: Journal: Appl.Microbiol.Biotechnol. / Year: 1990
Title: Molecular Cloning, Nucleotide Sequence and Expression in Escherichia Coli of the Beta-Cyclodextrin Glycosyltransferase Gene from Bacillus Circulans Strain No. 8
Authors: Nitschke, L. / Heeger, K. / Bender, H. / Schulz, G.E.
History
DepositionJun 6, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYCLODEXTRIN GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6367
Polymers74,5531
Non-polymers1,0836
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.000, 104.900, 113.700
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 CYCLODEXTRIN GLYCOSYLTRANSFERASE / CYCLODEXTRIN GLUCANOTRANSFERASE / CGTASE / 1 / 4-ALPHA-D-GLUCAN\:1 / 4-ALPHA-D- ...CYCLODEXTRIN GLUCANOTRANSFERASE / CGTASE / 1 / 4-ALPHA-D-GLUCAN\:1 / 4-ALPHA-D-GLUCOPYRANOSYLTRANSFERASE (CYCLIZING)


Mass: 74552.984 Da / Num. of mol.: 1 / Mutation: L194T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Strain: 8 / Cellular location: EXTRACELLULARGlossary of biology / Production host: Escherichia coli (E. coli) / Strain (production host): TG1
References: UniProt: P30920, cyclomaltodextrin glucanotransferase
#2: Polysaccharide 4-amino-4,6-dideoxy-beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 325.313 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122m-1b_1-5_4*N]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-OPG / OXIRANPSEUDOGLUCOSE


Mass: 176.167 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H12O5
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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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: 3.73 Å3/Da / Density % sol: 67 %
Crystal growpH: 6.9 / Details: pH 6.9
Crystal grow
*PLUS
pH: 6.7 / Method: vapor diffusion, hanging drop / Details: Hofmann, B.E., (1989) J.Mol.Biol., 209, 793.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 %(v/v)protein solution1drop
27-15 mg/mlCGTase1drop
350 mMTris-HCl1drop
40.5 %PEG15001drop
50.9-1.0 Mammonium sulphate1reservoir
67-15 mg/mlCGTase1reservoir
750 mMTris-HCl1reservoir
80.5 %PEG15001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jul 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→27.4 Å / Num. obs: 30356 / % possible obs: 92 % / Rsym value: 0.087
Reflection shellHighest resolution: 2.6 Å / % possible all: 69
Reflection
*PLUS
Rmerge(I) obs: 0.087
Reflection shell
*PLUS
% possible obs: 69 %

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
XDSdata reduction
X-PLOR3.8phasing
RefinementMethod to determine structure: X-PLOR WITH WILD-TYPE MODEL / Resolution: 2.6→27 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.246 -RANDOM
Rwork0.167 --
obs0.167 30356 -
Displacement parametersBiso mean: 16.5 Å2
Refinement stepCycle: LAST / Resolution: 2.6→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5266 0 69 201 5536
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM3.CHOTOPH3.CHO
X-RAY DIFFRACTION4HOXA.PARAMTOPHINH_MOD.GLC
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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