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- PDB-4gkl: Crystal structure of a noncanonic maltogenic alpha-amylase AmyB f... -

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Basic information

Entry
Database: PDB / ID: 4gkl
TitleCrystal structure of a noncanonic maltogenic alpha-amylase AmyB from Thermotoga neapolitana
ComponentsAlpha-amylase
KeywordsHYDROLASE / (alpha/beta)8 barrel / maltogenic alpha-amylase
Function / homology
Function and homology information


catalytic activity / carbohydrate metabolic process
Similarity search - Function
Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like ...Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermotoga neapolitana (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHa, N.C. / Jun, S.Y. / Kim, J.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structure of a novel alpha-amylase AmyB from Thermotoga neapolitana that produces maltose from the nonreducing end of polysaccharides
Authors: Jun, S.Y. / Kim, J.S. / Choi, K.H. / Cha, J. / Ha, N.C.
History
DepositionAug 13, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Mar 20, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-amylase
B: Alpha-amylase


Theoretical massNumber of molelcules
Total (without water)100,2272
Polymers100,2272
Non-polymers00
Water4,396244
1
A: Alpha-amylase


Theoretical massNumber of molelcules
Total (without water)50,1131
Polymers50,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alpha-amylase


Theoretical massNumber of molelcules
Total (without water)50,1131
Polymers50,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.880, 74.449, 108.900
Angle α, β, γ (deg.)90.00, 107.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-amylase /


Mass: 50113.492 Da / Num. of mol.: 2 / Fragment: alpha-amylase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga neapolitana (bacteria) / Gene: amyB / Production host: Escherichia coli (E. coli) / References: UniProt: B5ARZ9, alpha-amylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.58 Å3/Da / Density % sol: 52.25 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Sodium acetate, 2M sodium formate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 8, 2011
RadiationMonochromator: Double MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 37665 / Num. obs: 35640 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.4→2.44 Å / % possible all: 86.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DHU

3dhu


Resolution: 2.4→19.98 Å / SU ML: 0.34 / σ(F): 1.54 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2633 1981 5.26 %RANDOM
Rwork0.1974 ---
obs0.201 35640 93.93 %-
all-37665 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.47 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.3982 Å2-0 Å210.6891 Å2
2---11.9694 Å2-0 Å2
3---4.5713 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7021 0 0 244 7265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087208
X-RAY DIFFRACTIONf_angle_d1.2789740
X-RAY DIFFRACTIONf_dihedral_angle_d18.0522700
X-RAY DIFFRACTIONf_chiral_restr0.0911015
X-RAY DIFFRACTIONf_plane_restr0.0061250
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.45770.32741270.2671223684
2.4577-2.5240.3491330.2437236088
2.524-2.59820.26231270.234236987
2.5982-2.68180.31491360.2327242290
2.6818-2.77740.30641340.2369247692
2.7774-2.88830.34411390.2403257195
2.8883-3.01940.28521490.2223259296
3.0194-3.1780.27451500.2065259797
3.178-3.37620.27851410.1931259396
3.3762-3.63540.24591460.1854261596
3.6354-3.99860.23691480.1744266198
3.9986-4.57120.21161470.1668269599
4.5712-5.73650.19211480.1791272099
5.7365-19.98030.26591560.22275399

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