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- PDB-1jae: STRUCTURE OF TENEBRIO MOLITOR LARVAL ALPHA-AMYLASE -

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Basic information

Entry
Database: PDB / ID: 1jae
TitleSTRUCTURE OF TENEBRIO MOLITOR LARVAL ALPHA-AMYLASE
ComponentsALPHA-AMYLASE
KeywordsGLYCOSIDASE / ALPHA-AMYLASE / CARBOHYDRATE METABOLISM / ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE / HYDROLASE
Function / homology
Function and homology information


alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / chloride ion binding / calcium ion binding
Similarity search - Function
Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / 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
Biological speciesTenebrio molitor (yellow mealworm)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsStrobl, S. / Maskos, K. / Betz, M. / Wiegand, G. / Huber, R. / Gomis-Rueth, F.X. / Frank, G. / Glockshuber, R.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of yellow meal worm alpha-amylase at 1.64 A resolution.
Authors: Strobl, S. / Maskos, K. / Betz, M. / Wiegand, G. / Huber, R. / Gomis-Ruth, F.X. / Glockshuber, R.
#1: Journal: FEBS Lett. / Year: 1997
Title: The Alpha-Amylase from the Yellow Meal Worm: Complete Primary Structure, Crystallization and Preliminary X-Ray Analysis
Authors: Strobl, S. / Gomis-Ruth, F.X. / Maskos, K. / Frank, G. / Huber, R. / Glockshuber, R.
History
DepositionSep 30, 1997Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence / Category: entity_poly / pdbx_struct_mod_residue
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id
Revision 2.1Apr 3, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)51,3393
Polymers51,2631
Non-polymers762
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.240, 93.460, 96.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ALPHA-AMYLASE


Mass: 51263.066 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 - 471 / Source method: isolated from a natural source / Source: (natural) Tenebrio molitor (yellow mealworm) / References: UniProt: P56634, alpha-amylase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Compound detailsC-TERMINUS - LEU 496: N-TERMINUS BLOCKED AGAINST AMINOPEPTIDASE ACTIVITY BY GLUTAMINE CYCLATION TO ...C-TERMINUS - LEU 496: N-TERMINUS BLOCKED AGAINST AMINOPEPTIDASE ACTIVITY BY GLUTAMINE CYCLATION TO RENDER PYROGLUTAMATE.
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45 %
Description: UNRELEASED COORDINATES KINDLY CEASED BY M.MACHIUS AND G.WIEGAND
Crystal growpH: 6.5
Details: 200 MM SODIUM ACETATE, 100 MM BISTRIS-HCL PH 6.5 30% W/V PEG 8000
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 5.4 / Method: vapor diffusion, hanging drop / Details: Strobl, S., (1997) FEBS Lett., 409, 109.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mMacetic acid/NaOH1drop
20.1 mM1dropCaCl2
363 mg/mlprotein1drop
4200 mMsodium acetate1reservoir
5100 mMBis-Tris-HCl1reservoir
630 %(w/v)PEG80001reservoir

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. obs: 58219 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.057
Reflection
*PLUS
Num. measured all: 244244
Reflection shell
*PLUS
Highest resolution: 1.64 Å / Lowest resolution: 1.69 Å / % possible obs: 99.2 %

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Processing

Software
NameVersionClassification
MOSFLMV. 5.23data reduction
CCP4data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PIG PANCREATIC ALPHA AMYLASE

Resolution: 1.65→7 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.206 -7 %
Rwork0.177 --
obs0.177 55053 -
Displacement parametersBiso mean: 15.3 Å2
Refinement stepCycle: LAST / Resolution: 1.65→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3606 0 2 261 3869
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.482
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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

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