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- PDB-1a47: CGTASE FROM THERMOANAEROBACTERIUM THERMOSULFURIGENES EM1 IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 1a47
TitleCGTASE FROM THERMOANAEROBACTERIUM THERMOSULFURIGENES EM1 IN COMPLEX WITH A MALTOHEXAOSE INHIBITOR
ComponentsCYCLODEXTRIN GLYCOSYLTRANSFERASE
KeywordsGLYCOSIDASE / THERMOSTABLE / FAMILY 13 GLYCOSYL HYDROLASE / LIGAND / SUBSTRATE / ACARBOSE
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 / alpha-maltotriose / Chem-ADH / Cyclomaltodextrin glucanotransferase
Similarity search - Component
Biological speciesThermoanaerobacterium thermosulfurigenes (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsUitdehaag, J.C.M. / Kalk, K.H. / Rozeboom, H.J. / Dijkstra, B.W.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: Engineering of cyclodextrin product specificity and pH optima of the thermostable cyclodextrin glycosyltransferase from Thermoanaerobacterium thermosulfurigenes EM1.
Authors: Wind, R.D. / Uitdehaag, J.C. / Buitelaar, R.M. / Dijkstra, B.W. / Dijkhuizen, L.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Crystal Structure at 2.3 A Resolution and Revised Nucleotide Sequence of the Thermostable Cyclodextrin Glycosyltransferase from Thermoanaerobacterium Thermosulfurigenes Em1
Authors: Knegtel, R.M. / Wind, R.D. / Rozeboom, H.J. / Kalk, K.H. / Buitelaar, R.M. / Dijkhuizen, L. / Dijkstra, B.W.
#2: Journal: Biochemistry / Year: 1996
Title: Structure of Cyclodextrin Glycosyltransferase Complexed with a Maltononaose Inhibitor at 2.6 Angstrom Resolution. Implications for Product Specificity
Authors: Strokopytov, B. / Knegtel, R.M. / Penninga, D. / Rozeboom, H.J. / Kalk, K.H. / Dijkhuizen, L. / Dijkstra, B.W.
History
DepositionFeb 11, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 25, 2017Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_database_status / struct_conn / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_database_status.process_site / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Nov 20, 2019Group: Data collection / Derived calculations / Category: chem_comp / pdbx_struct_conn_angle / struct_conn / Item: _chem_comp.type
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)77,0737
Polymers75,4981
Non-polymers1,5756
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.996, 97.789, 116.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CYCLODEXTRIN GLYCOSYLTRANSFERASE / CGTASE


Mass: 75498.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium thermosulfurigenes (bacteria)
Strain: EM1 / Cellular location: EXTRACELLULARGlossary of biology / Gene: AMYA / Plasmid: PCT2 / Cellular location (production host): EXTRACELLULAR / Gene (production host): AMYA / Production host: Escherichia coli (E. coli) / Strain (production host): PC1990
References: UniProt: P26827, cyclomaltodextrin glucanotransferase

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Sugars , 3 types, 3 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DQuipa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-4,6-deoxy-Glcp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
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

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Non-polymers , 3 types, 188 molecules

#5: Chemical ChemComp-ADH / 1-AMINO-2,3-DIHYDROXY-5-HYDROXYMETHYL CYCLOHEX-5-ENE


Mass: 159.183 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C7H13NO3
#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsELECTRON DENSITY IN THE ACTIVE SITE, BETWEEN SUBSITES -1 AND +1 (THE SCISSILE BOND), IS NOT ...ELECTRON DENSITY IN THE ACTIVE SITE, BETWEEN SUBSITES -1 AND +1 (THE SCISSILE BOND), IS NOT COMPATIBLE WITH EITHER A CONTINUOUS MALTOHEXAOSE INHIBITOR, A COVALENT INTERMEDIATE + ACCEPTOR, OR TWO SEPARATE TRIOSES. PROBABLY AN AVERAGE IS OBSERVED, BUT THE LOW RESOLUTION DOESN'T ALLOW THIS TO BE MODELLED. TO ENSURE A REASONABLE FIT TO THE ELECTRON DENSITY, REFINEMENT RESTRAINTS ON THE SCISSILE BOND WERE LOOSENED, RESULTING IN A LONGER SCISSILE BOND (2.3 A, NORMAL: 1.47 A).

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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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growpH: 7.7
Details: 21% SATURATED AMMONIUM SULFATE, 100 MM TRIS, PH 7.7
Crystal grow
*PLUS
pH: 7.6 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
121 %satammonium sulfate11
2100 mMTris-HCl11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: Apr 8, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.56→45.07 Å / Num. obs: 25423 / % possible obs: 91.1 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.0682 / Rsym value: 0.07 / Net I/σ(I): 9.3
Reflection shellResolution: 2.56→2.58 Å / Redundancy: 3 % / Rmerge(I) obs: 0.2155 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.22 / % possible all: 74.3
Reflection
*PLUS
Num. measured all: 181769
Reflection shell
*PLUS
% possible obs: 74.3 %

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Processing

Software
NameVersionClassification
BIOMOLmodel building
TNT5Drefinement
XDSdata reduction
BIOMOL(KBAPLY)data scaling
BIOMOLphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CIU

1ciu


Resolution: 2.56→8 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: R FREE THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: IDEAL PARAMETERS FOR GLUCOSE FROM TAKUSAGAWA & JACOBSON (1978), ACTA CRYST. B34:213-218, FOR ACARBOSE FROM STROKOPYTOV ET AL. (1995) BIOCHEMISTRY 34:2234-2240
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1956 7 %EVERY 14TH REFLECTION
Rwork0.186 ---
all0.191 25423 --
obs0.191 24483 84 %-
Refinement stepCycle: LAST / Resolution: 2.56→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5333 0 102 185 5620
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00355773
X-RAY DIFFRACTIONt_angle_deg0.97176018
X-RAY DIFFRACTIONt_dihedral_angle_d17.531410
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0071435
X-RAY DIFFRACTIONt_gen_planes0.00780330
X-RAY DIFFRACTIONt_it1.57155755
X-RAY DIFFRACTIONt_nbd0.00922740
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg17.50
X-RAY DIFFRACTIONt_plane_restr0.00730

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