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- PDB-1izk: Thermoactinomyces vulgaris R-47 alpha-amylase 1 mutant enzyme w398v -

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Basic information

Entry
Database: PDB / ID: 1izk
TitleThermoactinomyces vulgaris R-47 alpha-amylase 1 mutant enzyme w398v
Componentsamylase
KeywordsHYDROLASE / alpha-beta barrele
Function / homology
Function and homology information


neopullulanase / neopullulanase activity / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 13, N-terminal Ig-like domain / Alpha amylase, N-terminal ig-like 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 ...Glycoside hydrolase, family 13, N-terminal Ig-like domain / Alpha amylase, N-terminal ig-like 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
Biological speciesThermoactinomyces vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOhtaki, A. / Iguchi, A. / Mizuno, M. / Tonozuka, T. / Sakano, Y. / Kamitori, S.
CitationJournal: CARBOHYDR.RES. / Year: 2003
Title: Mutual conversion of substrate specificities of Thermoactinomyces vulgaris R-47 alpha-amylases TVAI and TVAII by site-directed mutagenesis
Authors: Ohtaki, A. / Iguchi, A. / Mizuno, M. / Tonozuka, T. / Sakano, Y. / Kamitori, S.
History
DepositionOct 3, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2003Provider: 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 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1434
Polymers71,0231
Non-polymers1203
Water7,386410
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.720, 50.820, 108.820
Angle α, β, γ (deg.)90.00, 104.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein amylase / alpha-amylase I


Mass: 71023.211 Da / Num. of mol.: 1 / Mutation: w398v
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Strain: R-47 / Production host: Escherichia coli (E. coli) / References: UniProt: Q60053, alpha-amylase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.31 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG20000, MES, CACL2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Details: Kondo, S., (2000) Protein Pept. Letters, 7, 197.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 7, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→25.41 Å / Num. all: 412389 / Num. obs: 412389 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 9.3 Å2 / Rmerge(I) obs: 0.072
Reflection
*PLUS
Num. obs: 33199 / Num. measured all: 412389

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→25.41 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 4113635.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3398 10.2 %RANDOM
Rwork0.192 ---
all0.196 33199 --
obs0.196 33199 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.7555 Å2 / ksol: 0.404487 e/Å3
Displacement parametersBiso mean: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å20 Å20.3 Å2
2--1.11 Å20 Å2
3----4.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.2→25.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5030 0 3 410 5443
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.161.5
X-RAY DIFFRACTIONc_mcangle_it1.712
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_scangle_it2.342.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 584 10.7 %
Rwork0.214 4890 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.237 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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