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- PDB-3kwx: Chemically modified Taka alpha-amylase -

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Basic information

Entry
Database: PDB / ID: 3kwx
TitleChemically modified Taka alpha-amylase
ComponentsAlpha-amylase A type-1/2
KeywordsHYDROLASE / HYDROLASE(O-GLYCOSYL) / 1 / 4-alpha-D-glucan glucanohydrolase / CHEMICAL MODIFICATION / ARGININEMETHYLESTER / Carbohydrate metabolism / Disulfide bond / Glycoprotein / Glycosidase / Metal-binding
Function / homology
Function and homology information


cell wall-bounded periplasmic space / hyphal septin band / spitzenkorper / fungal-type cell wall / alpha-amylase / cell septum / carbohydrate catabolic process / alpha-amylase activity / calcium ion binding / extracellular region
Similarity search - Function
Alpha-amylase, domain C / Alpha-amylase, domain C / Alpha-amylase-like / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases ...Alpha-amylase, domain C / Alpha-amylase, domain C / Alpha-amylase-like / Alpha amylase / 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
Alpha-amylase A type-1/2
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSiddiqui, K.S. / Harrop, S.J. / Poljak, A. / De Francisci, D. / Guerriero, G. / Pilak, O. / Burg, D. / Raftery, M.J. / Parkin, D.M. / Trewhella, J. / Cavicchioli, R.
CitationJournal: To be Published
Title: A Modified alpha-amylase with a molten-globule state has enhanced thermal stability
Authors: Siddiqui, K.S. / Poljak, A. / De Francisci, D. / Guerriero, G. / Pilak, O. / Burg, D. / Raftery, M.J. / Parkin, D.M. / Trewhella, J. / Cavicchioli, R.
History
DepositionDec 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Alpha-amylase A type-1/2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7873
Polymers52,5261
Non-polymers2612
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.727, 120.727, 115.676
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Alpha-amylase A type-1/2 / Taka-amylase A / TAA / 1 / 4-alpha-D-glucan glucanohydrolase


Mass: 52525.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus oryzae (mold) / References: UniProt: P0C1B3, alpha-amylase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 4.63 Å3/Da / Density % sol: 73.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 20% PEG 4000, 0.4M AMSO4, 0.1M MES pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2008 / Details: MIRROR
RadiationMonochromator: yes / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→36.18 Å / Num. obs: 38486 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 54.5 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 17.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 3.9 / Num. unique all: 5566 / Rsym value: 0.523 / % possible all: 99.9

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Processing

Software
NameClassification
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GVY

2gvy


Resolution: 2.4→36.177 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.04 / σ(I): 0 / Phase error: 21.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 1945 5.14 %RANDOM
Rwork0.175 ---
obs0.1768 37823 98.2 %-
all-38486 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.375 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso mean: 48.987 Å2
Baniso -1Baniso -2Baniso -3
1-6.011 Å2-0 Å2-0 Å2
2--6.011 Å20 Å2
3----12.023 Å2
Refinement stepCycle: LAST / Resolution: 2.4→36.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 15 275 3976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083801
X-RAY DIFFRACTIONf_angle_d1.0715186
X-RAY DIFFRACTIONf_dihedral_angle_d16.7831297
X-RAY DIFFRACTIONf_chiral_restr0.073568
X-RAY DIFFRACTIONf_plane_restr0.004671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.48590.2841790.24243419X-RAY DIFFRACTION94
2.4859-2.58540.27371780.21083443X-RAY DIFFRACTION96
2.5854-2.7030.27271980.20623528X-RAY DIFFRACTION97
2.703-2.84540.24131960.20193526X-RAY DIFFRACTION98
2.8454-3.02360.2381980.20143595X-RAY DIFFRACTION99
3.0236-3.2570.24662000.20273567X-RAY DIFFRACTION99
3.257-3.58450.22471970.18063634X-RAY DIFFRACTION100
3.5845-4.10250.18281790.15123683X-RAY DIFFRACTION100
4.1025-5.16630.16092260.13123651X-RAY DIFFRACTION100
5.1663-36.18090.18531940.16633832X-RAY DIFFRACTION100

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