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- PDB-1bvz: ALPHA-AMYLASE II (TVAII) FROM THERMOACTINOMYCES VULGARIS R-47 -

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Basic information

Entry
Database: PDB / ID: 1bvz
TitleALPHA-AMYLASE II (TVAII) FROM THERMOACTINOMYCES VULGARIS R-47
ComponentsPROTEIN (ALPHA-AMYLASE II)
KeywordsHYDROLASE
Function / homology
Function and homology information


neopullulanase / neopullulanase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 13, N-terminal Ig-like domain / Alpha amylase, N-terminal ig-like domain / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain ...Glycoside hydrolase, family 13, N-terminal Ig-like domain / Alpha amylase, N-terminal ig-like domain / Maltogenic Amylase, C-terminal / Maltogenic Amylase, C-terminal domain / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / 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 / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermoactinomyces vulgaris (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.6 Å
AuthorsKamitori, S. / Kondo, S. / Okuyama, K. / Yokota, T. / Shimura, Y. / Tonozuka, T. / Sakano, Y.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution.
Authors: Kamitori, S. / Kondo, S. / Okuyama, K. / Yokota, T. / Shimura, Y. / Tonozuka, T. / Sakano, Y.
History
DepositionSep 22, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (ALPHA-AMYLASE II)
B: PROTEIN (ALPHA-AMYLASE II)


Theoretical massNumber of molelcules
Total (without water)135,1082
Polymers135,1082
Non-polymers00
Water8,611478
1
A: PROTEIN (ALPHA-AMYLASE II)


Theoretical massNumber of molelcules
Total (without water)67,5541
Polymers67,5541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (ALPHA-AMYLASE II)


Theoretical massNumber of molelcules
Total (without water)67,5541
Polymers67,5541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.600, 117.900, 114.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, 0.0026, 0.0029), (0.0037, 0.8724, 0.4889), (-0.0013, 0.4889, -0.8724)
Vector: 119.2336, -24.3867, 92.5498)

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Components

#1: Protein PROTEIN (ALPHA-AMYLASE II)


Mass: 67554.109 Da / Num. of mol.: 2 / Fragment: N,A,B.C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q08751, neopullulanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 58.7 %
Crystal growpH: 6.1 / Details: pH 6.1
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 11 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12 %(w/v)PEG60001reservoir
22.5 mM1reservoirCaCl2
320 mMMES1reservoirpH6.1
420 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Apr 15, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 43840 / % possible obs: 91.8 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 5.31
Reflection shellResolution: 2.6→2.73 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.286 / % possible all: 78.1
Reflection
*PLUS
Num. measured all: 91759

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
CCP4data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.6→7 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.272 3861 10 %RANDOM
Rwork0.196 ---
obs0.196 38661 85 %-
Displacement parametersBiso mean: 30.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 7 Å
Refinement stepCycle: LAST / Resolution: 2.6→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9552 0 0 478 10030
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.4
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: 2.6→2.69 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.335 287 9.5 %
Rwork0.219 2441 -
obs--61 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 7 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.4
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Rfactor Rfree: 0.335 / % reflection Rfree: 9.5 % / Rfactor Rwork: 0.219

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