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- PDB-1cgt: STRUCTURE OF CYCLODEXTRIN GLYCOSYLTRANSFERASE REFINED AT 2.0 ANGS... -

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Basic information

Entry
Database: PDB / ID: 1cgt
TitleSTRUCTURE OF CYCLODEXTRIN GLYCOSYLTRANSFERASE REFINED AT 2.0 ANGSTROMS RESOLUTION
ComponentsCYCLODEXTRIN GLYCOSYL-TRANSFERASE
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 / 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 / Resolution: 2 Å
AuthorsKlein, C. / Schulz, G.E.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Structure of cyclodextrin glycosyltransferase refined at 2.0 A resolution.
Authors: Klein, C. / Schulz, G.E.
#1: Journal: Protein Eng. / Year: 1990
Title: Engineering a Heavy Atom Derivative for the X-Ray Structure Analysis of Cyclodextrin Glycosyltransferase
Authors: Klein, C. / Vogel, W. / Bender, H. / Schulz, G.E.
#2: 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.
#3: Journal: J.Mol.Biol. / Year: 1989
Title: Three-Dimensional Structure of Cyclodextrin Glycosyltransferase from Bacillus Circulans at 3.4 Angstroms Resolution
Authors: Hofmann, B.E. / Bender, H. / Schulz, G.E.
History
DepositionJun 10, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 650HELIX HELIX STRAND H1 IS A NONHELICAL SEGMENT BETWEEN ASP 63 AND ASN 64.
Remark 700SHEET THIS MOLECULE CONTAINS ONE BIFURCATED SHEET. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET ...SHEET THIS MOLECULE CONTAINS ONE BIFURCATED SHEET. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, THE TWO SHEETS, S11 AND S12, ARE DEFINED HAVING STRANDS 1, 2, 3, IN COMMON.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYCLODEXTRIN GLYCOSYL-TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6453
Polymers74,5651
Non-polymers802
Water10,593588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.800, 104.700, 114.000
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 505 / 3: CIS PROLINE - PRO 623 / 4: CIS PROLINE - PRO 633

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Components

#1: Protein CYCLODEXTRIN GLYCOSYL-TRANSFERASE


Mass: 74565.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria)
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.: 588 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE BELOW IS THAT DETERMINED BY THE AUTHORS, SEE REFERENCE 3 ABOVE.

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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 grow
*PLUS
pH: 6.7 / Method: vapor diffusion, hanging drop
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

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. obs: 70862 / % possible obs: 96 % / Num. measured all: 387934 / Rmerge(I) obs: 0.119

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→7 Å /
RfactorNum. reflection
Rwork0.166 -
obs0.166 70862
Refinement stepCycle: LAST / Resolution: 2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5267 0 2 588 5857
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.78
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 7 Å / Num. reflection all: 70862 / σ(I): 0 / Rfactor all: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.78

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