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- PDB-1ciu: THERMOSTABLE CGTASE FROM THERMOANAEROBACTERIUM THERMOSULFURIGENES... -

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Basic information

Entry
Database: PDB / ID: 1ciu
TitleTHERMOSTABLE CGTASE FROM THERMOANAEROBACTERIUM THERMOSULFURIGENES EM1 AT PH 8.0.
ComponentsCYCLODEXTRIN GLYCOSYLTRANSFERASE
KeywordsGLYCOSIDASE / THERMOSTABLE
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 / 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 speciesThermoanaerobacterium thermosulfurigenes (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsKnegtel, R.M.A. / Dijkstra, B.W.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Crystal structure at 2.3 A resolution and revised nucleotide sequence of the thermostable cyclodextrin glycosyltransferase from Thermonanaerobacterium thermosulfurigenes EM1.
Authors: Knegtel, R.M. / Wind, R.D. / Rozeboom, H.J. / Kalk, K.H. / Buitelaar, R.M. / Dijkhuizen, L. / Dijkstra, B.W.
#1: Journal: Biochemistry / Year: 1995
Title: X-Ray Structure of Cyclodextrin Glycosyltransferase Complexed with Acarbose. Implications for the Catalytic Mechanism of Glycosidases
Authors: Strokopytov, B. / Penninga, D. / Rozeboom, H.J. / Kalk, K.H. / Dijkhuizen, L. / Dijkstra, B.W.
#2: 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.
#3: Journal: J.Mol.Biol. / Year: 1990
Title: Maltodextrin-Dependent Crystallization of Cyclomalto-Dextrin Glucanotransferase from Bacillus Circulans
Authors: Lawson, C.L.L. / Bergsma, J. / Bruinenberg, P.M. / De Vries, G. / Dijkhuizen, L. / Dijkstra, B.W.
History
DepositionOct 23, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

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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)75,5783
Polymers75,4981
Non-polymers802
Water6,179343
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.900, 97.400, 115.800
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 621 / 4: CIS PROLINE - PRO 631

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Components

#1: Protein CYCLODEXTRIN GLYCOSYLTRANSFERASE / CGTASE


Mass: 75498.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermoanaerobacterium thermosulfurigenes (bacteria)
References: UniProt: P26827, 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.: 343 / 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: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal
*PLUS
Density % sol: 59 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 8 / PH range high: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.4 mg/mlprotein1drop
210 mMsodium acetate1drop
319-22 %satammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jan 23, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 3.8 % / Rmerge(I) obs: 0.061
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 34.3 Å / Num. obs: 31189 / % possible obs: 82.4 % / Num. measured all: 119291 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.34 Å / % possible obs: 66.6 %

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Processing

Software
NameClassification
TNTrefinement
XDSdata reduction
RefinementResolution: 2.3→6 Å / σ(F): 0 /
RfactorNum. reflection
Rfree0.2 -
obs0.179 26193
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5333 0 2 343 5678
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.004
X-RAY DIFFRACTIONt_angle_deg0.9
X-RAY DIFFRACTIONt_dihedral_angle_d18.6
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.009
X-RAY DIFFRACTIONt_it1.37
X-RAY DIFFRACTIONt_nbd0.019
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.009

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