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- PDB-7cgt: RAMEB COMPLEX OF CYCLODEXTRIN GLYCOSYLTRANSFERASE MUTANT -

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Basic information

Entry
Database: PDB / ID: 7cgt
TitleRAMEB COMPLEX OF CYCLODEXTRIN GLYCOSYLTRANSFERASE MUTANT
ComponentsCYCLODEXTRIN GLYCOSYLTRANSFERASE
KeywordsGLYCOSYLTRANSFERASE / STARCH DEGRADATION / CYCLODEXTRIN
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cyclomaltodextrin glucanotransferase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / X-PLOR WITH WILD-TYPE MODEL / Resolution: 3 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 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.pdbx_dist_value / _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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYCLODEXTRIN GLYCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6013
Polymers74,5211
Non-polymers802
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.000, 104.800, 113.600
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: 74521.031 Da / Num. of mol.: 1 / Mutation: D229A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Strain: 8 / Cellular location: EXTRACELLULAR / Production host: Escherichia coli (E. coli) / Strain (production host): TG1
References: UniProt: P30920, cyclomaltodextrin glucanotransferase
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.57 %
Crystal growpH: 6.9
Details: pH 6.9 THE SUBMITTED PDB FILE RESULTED FROM A SOAK OF CGTASE MUTANT D229A WITH A 1.8 TIMES RANDOMLY METHYLATED BETA-CYCLODEXTRIN (RAMEB). THE STRUCTURE WAS REFINED WITH A NON-METHYLATED BETA- ...Details: pH 6.9 THE SUBMITTED PDB FILE RESULTED FROM A SOAK OF CGTASE MUTANT D229A WITH A 1.8 TIMES RANDOMLY METHYLATED BETA-CYCLODEXTRIN (RAMEB). THE STRUCTURE WAS REFINED WITH A NON-METHYLATED BETA-CYCLODEXTRIN MODEL WHICH IS NOT INCLUDED IN THE PDB FILE BECAUSE OF INSUFFICIENT DENSITY.
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: Aug 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→35.6 Å / Num. obs: 18086 / % possible obs: 82.5 %
Reflection shellHighest resolution: 3 Å / % possible all: 58

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: X-PLOR WITH WILD-TYPE MODEL / Resolution: 3→10 Å / Cross valid method: THROUGHOUT
Details: THE STRUCTURE WAS REFINED WITH A BETA-CYCLODEXTRIN MODEL WHICH IS NOT INCLUDED IN THE SUBMITTED PDB FILE.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 --RANDOM
Rwork0.165 ---
obs0.165 17511 82 %-
Displacement parametersBiso mean: 13.1 Å2
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5264 0 2 99 5365
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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

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