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- PDB-1pam: CYCLODEXTRIN GLUCANOTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1pam
TitleCYCLODEXTRIN GLUCANOTRANSFERASE
ComponentsCYCLODEXTRIN GLUCANOTRANSFERASE
KeywordsGLYCOSYLTRANSFERASE / TRANSFERASE
Function / homology
Function and homology information


cyclomaltodextrin glucanotransferase activity / cyclomaltodextrin glucanotransferase / starch binding / alpha-amylase activity / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function
Carbohydrate binding module family 20 / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Starch binding domain / Carbohydrate-binding-like fold / Alpha-amylase, C-terminal domain / Aamy_C / Alpha amylase, C-terminal all-beta domain / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase ...Carbohydrate binding module family 20 / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Starch binding domain / Carbohydrate-binding-like fold / Alpha-amylase, C-terminal domain / Aamy_C / Alpha amylase, C-terminal all-beta domain / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase / IPT/TIG domain / IPT domain / Alpha amylase, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, family 13, catalytic domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Immunoglobulin-like fold / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cyclomaltodextrin glucanotransferase
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHarata, K. / Haga, K. / Nakamura, A. / Aoyagi, M. / Yamane, K.
CitationJournal: 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.
Authors: Harata, K. / Haga, K. / Nakamura, A. / Aoyagi, M. / Yamane, K.
History
DepositionJul 8, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site

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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)150,6206
Polymers150,4602
Non-polymers1604
Water14,502805
1
A: CYCLODEXTRIN GLUCANOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3103
Polymers75,2301
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYCLODEXTRIN GLUCANOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3103
Polymers75,2301
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.930, 74.450, 79.120
Angle α, β, γ (deg.)85.20, 105.00, 101.00
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) / Strain: 1011 / Description: ALKALOPHILIC BACILLUS SP. 1011 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 805 / 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: 9

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growpH: 5.6
Details: 1% PROTEIN, 20% PEG3000, 20% 2 PROPANOL,0.1M NA CITRATE, PH 5.6
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %(w/v)PEG300011
220 %(v/v)2-propanol solution11
30.1 Msodium citrate11

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→29.6 Å / Num. obs: 111795 / % possible obs: 86.1 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.08

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Processing

Software
NameClassification
MADNESdata collection
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: B. STEAROTHERMOPHILUS CGTASE

Resolution: 1.8→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.211 -5 %
Rwork0.161 --
obs0.161 101409 74.5 %
Displacement parametersBiso mean: 22.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10624 0 4 805 11433
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg2.65
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.1
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
LS refinement shellResolution: 1.8→1.83 Å
RfactorNum. reflection% reflection
Rfree0.227 --
Rwork0.257 577 -
obs--9 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1

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