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- PDB-1hvx: BACILLUS STEAROTHERMOPHILUS ALPHA-AMYLASE -

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Basic information

Entry
Database: PDB / ID: 1hvx
TitleBACILLUS STEAROTHERMOPHILUS ALPHA-AMYLASE
ComponentsALPHA-AMYLASE
KeywordsHYDROLASE / GLYCOSYLTRANSFERASE / ALPHA-AMYLASE / STARCH DEGRADATION / ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE / THERMOSTABILITY
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / calcium ion binding / extracellular region
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #140 / Alpha-amylase, thermostable / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Elongation Factor Tu (Ef-tu); domain 3 / Glycosyl hydrolase, all-beta ...Elongation Factor Tu (Ef-tu); domain 3 - #140 / Alpha-amylase, thermostable / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Elongation Factor Tu (Ef-tu); domain 3 / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSuvd, D. / Fujimoto, Z. / Takase, K. / Matsumura, M. / Mizuno, H.
Citation
Journal: J.Biochem. / Year: 2001
Title: Crystal structure of Bacillus stearothermophilus alpha-amylase: possible factors determining the thermostability.
Authors: Suvd, D. / Fujimoto, Z. / Takase, K. / Matsumura, M. / Mizuno, H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Purification, crystallization and preliminary X-ray crystallographic study of alpha-amylase from Bacillus stearothermophilus.
Authors: Suvd, D. / Takase, K. / Fujiimoto, Z. / Matsumura, M. / Mizuno, H.
#2: Journal: J.Mol.Biol. / Year: 1995
Title: Crystal structure of calcium-depleted Bacillus licheniformis alpha-amylase at 2.2 A resolution.
Authors: Machius, M. / Wiegand, G. / Huber, R.
#3: Journal: Structure / Year: 1998
Title: ACTIVATION OF BACILLUS LICHENIFORMIS ALPHA-AMYLASE THROUGH A DISORDER-->ORDER TRANSITION OF THE SUBSTRATE-BINDING SITE MEDIATED BY A CALCIUM-SODIUM-CALCIUM METAL TRIAD
Authors: Machius, M. / Declerck, N. / Huber, R. / Wiegand, R.
History
DepositionJan 8, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 15, 2012Group: Database references
Revision 1.4Nov 6, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-AMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0345
Polymers58,8901
Non-polymers1434
Water5,765320
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.550, 93.119, 53.275
Angle α, β, γ (deg.)90.00, 109.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ALPHA-AMYLASE


Mass: 58890.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: AMYT631 / Plasmid: PTUB617 / Production host: Bacillus subtilis (bacteria) / Strain (production host): A631 / References: UniProt: P06279, alpha-amylase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS A DIFFERENCE BETWEEN THE DEPOSITORS DATA(250Y) AND THE GENETIC SEQUENCE(284D) IN THE ...THERE IS A DIFFERENCE BETWEEN THE DEPOSITORS DATA(250Y) AND THE GENETIC SEQUENCE(284D) IN THE P06279 ENTRY. THERE IS NO QUESTION FROM THE ELECTRON DENSITY THAT THIS RESIDUE IS NOT DATABASE SEQUENCE.

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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: 2.13 Å3/Da / Density % sol: 42.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: SODIUM ACETATE, CALCIUM CLORIDE, 2-PROPANOL, ACARBOSE , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
135 mMsodium acetate1reservoirpH4.6
235 mM1reservoirCaCl2
36.25 %(v/v)2-propanol1reservoir
41.23 %(w/v)acarbose1reservoir
510 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 30530 / Num. obs: 29849 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 2.8 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 21.7
Reflection shellResolution: 2→2.09 Å / Rmerge(I) obs: 0.202 / Num. unique all: 3026 / % possible all: 73

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→8 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.1966 27048 random
Rwork0.154 --
all-29464 -
obs-28517 -
Displacement parametersBiso mean: 10.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.16 Å
Luzzati d res low-6 Å
Luzzati sigma a0.18 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3900 0 4 320 4224
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_improper_angle_d1.07
LS refinement shellResolution: 2→8 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.232 195 -
Rwork0.185 --
obs-3587 5.2 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.156
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 10.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.07
LS refinement shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / Rfactor Rfree: 0.232 / Rfactor Rwork: 0.185

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