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- PDB-1cxl: COMPLEX BETWEEN A COVALENT INTERMEDIATE AND BACILLUS CIRCULANS ST... -

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Basic information

Entry
Database: PDB / ID: 1cxl
TitleCOMPLEX BETWEEN A COVALENT INTERMEDIATE AND BACILLUS CIRCULANS STRAIN 251 CGTASE E257Q
ComponentsPROTEIN (CYCLODEXTRIN-GLYCOSYLTRANSFERASE)
KeywordsGLYCOSYLTRANSFERASE / GLYCOSYL HYDROLASE FAMILY 13 / ALPHA-AMYLASE FAMILY / INTERMEDIATE COMPLEX / 4- DEOXYMALTOTRIOSE
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 / Cyclomaltodextrin glucanotransferase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsUitdehaag, J.C.M. / Dijkstra, B.W.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: X-ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the alpha-amylase family.
Authors: Uitdehaag, J.C. / Mosi, R. / Kalk, K.H. / van der Veen, B.A. / Dijkhuizen, L. / Withers, S.G. / Dijkstra, B.W.
#1: Journal: Biochemistry / Year: 1998
Title: Reassessment of acarbose as a transition state analogue inhibitor of cyclodextrin glycosyltransferase.
Authors: Mosi, R. / Sham, H. / Uitdehaag, J.C. / Ruiterkamp, R. / Dijkstra, B.W. / Withers, S.G.
#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.
#3: Journal: J.Biol.Chem. / Year: 1995
Title: Crystallographic studies of the interaction of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 with natural substrates and products.
Authors: Knegtel, R.M. / Strokopytov, B. / Penninga, D. / Faber, O.G. / Rozeboom, H.J. / Kalk, K.H. / Dijkhuizen, L. / Dijkstra, B.W.
#4: 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. / van Montfort, R. / Strokopytov, B. / Rozeboom, H.J. / Kalk, K.H. / de Vries, G.E. / Penninga, D. / Dijkhuizen, L. / Dijkstra, B.W.
History
DepositionFeb 27, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0May 3, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / citation_author / diffrn_source / struct_conn
Item: _chem_comp.type / _citation.page_last ..._chem_comp.type / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
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_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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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 / _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.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 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
Revision 2.2Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (CYCLODEXTRIN-GLYCOSYLTRANSFERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5528
Polymers74,5581
Non-polymers1,9947
Water12,052669
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.071, 109.281, 65.335
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 PROTEIN (CYCLODEXTRIN-GLYCOSYLTRANSFERASE) / CGTASE


Mass: 74558.438 Da / Num. of mol.: 1 / Mutation: E257Q
Source method: isolated from a genetically manipulated source
Details: COVALENTLY BOUND REACTION INTERMEDIATE / Source: (gene. exp.) Bacillus circulans (bacteria) / Strain: 251
Description: MUTANTS WERE CONSTRUCTED IN ECOLI STRAIN MC1061
Plasmid: PDP66S / Gene (production host): CGT / Production host: Bacillus subtilis (bacteria) / Strain (production host): DB104A
References: UniProt: CDGU_BACCI, UniProt: P43379*PLUS, cyclomaltodextrin glucanotransferase

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Sugars , 3 types, 4 molecules

#2: Polysaccharide 4-deoxy-alpha-D-glucopyranose-(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
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a21d2h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-4-deoxy-Glcp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 4-deoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a21d2h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-4-deoxy-Glcp]{}}LINUCSPDB-CARE
#4: Polysaccharide 4-deoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranosyl fluoride


Type: oligosaccharide / Mass: 490.429 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a2122h-1a_1-5_1*F][a2122h-1a_1-5][a21d2h-1a_1-5]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp1fluoro]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-4-deoxy-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 672 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsCA: RESIDUES 688 AND 689 ARE CALCIUM IONS. GLC: THE GLC O1 ATOM IS CONNECTED TO THE C4 ATOM OF THE ...CA: RESIDUES 688 AND 689 ARE CALCIUM IONS. GLC: THE GLC O1 ATOM IS CONNECTED TO THE C4 ATOM OF THE PREVIOUS RESIDUE VIA AN ALPHA(1->4) GLYCOSIDIC BOND A LOOSE O1 IS A REDUCING END WITH ALPHA-ANOMERIC CONFIGURATION GLF IS IDENTICAL TO AN ALPHA GLUCOSE (GLC) EXCEPT THAT THE O1 ATOM HAS BEEN EXCHANGED BY A FLUORINE (F1) ATOM G4D IS IDENTICAL TO AN ALPHA GLUCOSE (GLC) EXCEPT THAT ITS O4 ATOM IS ABSENT (4-DEOXY)
Sequence detailsSER 400 AFTER REINTERPRETATION OF SEQUENCE DATA.

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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: 2.73 Å3/Da / Density % sol: 55 %
Description: ELECTRON DENSITY AT SUBSITES +1 AND +2 IS AMBIGUOUS, THREE WATER MOLECULES WERE PLACED THERE TO REPRESENT THIS DENSITY
Crystal growpH: 6.1
Details: CRYSTAL SOAKED FIRST IN 4-DEOXY MALTOSE,THEN IN 4-DEOXY MALTOTRIOSYL ALPHA- FLUORIDE, pH 6.10
Crystal
*PLUS
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion / Details: Lawson, C.L., (1990) J.Mol.Biol., 214, 807.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
128.7 mg/mlprotein1drop
250 mMammonium acetate1drop
350 mg/mlalpha-cyclodextrin1drop
460 %(v/v)MPD1reservoir
5100 mMsodium Hepes1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8838
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8838 Å / Relative weight: 1
ReflectionResolution: 1.81→58.54 Å / Num. obs: 73264 / % possible obs: 94.9 % / Observed criterion σ(I): 4 / Redundancy: 3.5 % / Biso Wilson estimate: 17.51 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 3 / % possible all: 49.9
Reflection
*PLUS
% possible obs: 94.9 %
Reflection shell
*PLUS
Highest resolution: 1.81 Å / Lowest resolution: 1.83 Å / % possible obs: 49.9 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CXI

1cxi


Resolution: 1.81→8 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: RFREE / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.19 3617 5 %EVERY
Rwork0.155 ---
obs-72330 94 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 216.9 Å2 / ksol: 0.774 e/Å3
Refinement stepCycle: LAST / Resolution: 1.81→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5264 0 122 677 6063
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00655304
X-RAY DIFFRACTIONt_angle_deg1.508752410
X-RAY DIFFRACTIONt_dihedral_angle_d16.1231320
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0061478
X-RAY DIFFRACTIONt_gen_planes0.01179530
X-RAY DIFFRACTIONt_it1.57455265
X-RAY DIFFRACTIONt_nbd0.01245380
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.81 Å / Lowest resolution: 8 Å / Rfactor obs: 0.155 / Rfactor Rfree: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_angle_deg10
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg016.12
X-RAY DIFFRACTIONt_planar_d80.006
X-RAY DIFFRACTIONt_plane_restr300.011

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