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- PDB-1i75: CRYSTAL STRUCTURE OF CYCLODEXTRIN GLUCANOTRANSFERASE FROM ALKALOP... -

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Basic information

Entry
Database: PDB / ID: 1i75
TitleCRYSTAL STRUCTURE OF CYCLODEXTRIN GLUCANOTRANSFERASE FROM ALKALOPHILIC BACILLUS SP.#1011 COMPLEXED WITH 1-DEOXYNOJIRIMYCIN
ComponentsCYCLODEXTRIN GLUCANOTRANSFERASE
KeywordsTRANSFERASE / PROTEIN-INHIBITOR COMPLEX
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
1-DEOXYNOJIRIMYCIN / Cyclomaltodextrin glucanotransferase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKanai, R. / Haga, K. / Yamane, K. / Harata, K.
Citation
Journal: J.Biochem.(Tokyo) / Year: 2001
Title: Crystal structure of cyclodextrin glucanotransferase from alkalophilic Bacillus sp. 1011 complexed with 1-deoxynojirimycin at 2.0 A resolution.
Authors: Kanai, R. / Haga, K. / Yamane, K. / Harata, K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: X-ray Structure of Cyclodextrin Glucanotransferase from Alkalophilic Bacillus Sp.1011. Comparison of Two Independent Molecules at 1.8 A Resolution
History
DepositionMar 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYCLODEXTRIN GLUCANOTRANSFERASE
B: CYCLODEXTRIN GLUCANOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,27310
Polymers150,4602
Non-polymers8138
Water10,629590
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.780, 74.240, 79.030
Angle α, β, γ (deg.)85.03, 104.88, 101.02
Int Tables number1
Space group name H-MP1

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Components

#1: Protein CYCLODEXTRIN GLUCANOTRANSFERASE


Mass: 75230.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Gene: BACCGTA / Plasmid: PTUE254 / Production host: Escherichia coli (E. coli) / Strain (production host): ME8417
References: UniProt: P05618, cyclomaltodextrin glucanotransferase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NOJ / 1-DEOXYNOJIRIMYCIN / MORANOLINE / 1-Deoxynojirimycin


Mass: 163.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG3000, 2-Propanol, sodium citrate, calcium chloride, 1-deoxynojirimycin, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
210 mM1-deoxynojirimycin1drop
320 %(w/v)PEG30001reservoir
420 %(v/v)2-propanol1reservoir
5100 mMsodium citrate1reservoir
60.5 mMcalcium chloride1reservoir

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Dec 20, 1997 / Details: graphite monochromator
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→27.89 Å / Num. all: 106410 / Num. obs: 106410 / % possible obs: 81.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.076
Reflection shellResolution: 1.84→1.87 Å / Rmerge(I) obs: 0.206

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Processing

Software
NameVersionClassification
MADNESSdata collection
MERGEFdata reduction
X-PLORmodel building
X-PLOR3.1refinement
MADNESSdata reduction
MERGEFdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PAM

1pam


Resolution: 2→10 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: CHARMM
RfactorNum. reflection% reflectionSelection details
Rfree0.214 4621 -RANDOM
Rwork0.154 ---
obs-86468 81.5 %-
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10624 0 48 590 11262
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg2.7
LS refinement shellResolution: 2→2.03 Å
RfactorNum. reflection% reflection
Rfree0.257 179 -
Rwork0.209 --
obs-3111 66.3 %

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