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- PDB-1tmq: STRUCTURE OF TENEBRIO MOLITOR LARVAL ALPHA-AMYLASE IN COMPLEX WIT... -

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Basic information

Entry
Database: PDB / ID: 1tmq
TitleSTRUCTURE OF TENEBRIO MOLITOR LARVAL ALPHA-AMYLASE IN COMPLEX WITH RAGI BIFUNCTIONAL INHIBITOR
Components
  • PROTEIN (ALPHA-AMYLASE)
  • PROTEIN (RAGI BIFUNCTIONAL INHIBITOR)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ALPHA-AMYLASE / CARBOHYDRATE METABOLISM / ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE / HYDROLASE BIFUNCTIONAL ALPHA-AMYLASE/TRYPSIN INHIBITOR / COMPLEX (ENZYME- INHIBITOR) / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


alpha-amylase inhibitor activity / alpha-amylase / alpha-amylase activity / carbohydrate catabolic process / chloride ion binding / serine-type endopeptidase inhibitor activity / calcium ion binding / extracellular region
Similarity search - Function
Cereal seed allergen/trypsin and alpha-amylase inhibitor, conserved site / Cereal trypsin/alpha-amylase inhibitors family signature. / Cereal seed allergen/grain softness/trypsin and alpha-amylase inhibitor / Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Alpha-amylase, C-terminal domain ...Cereal seed allergen/trypsin and alpha-amylase inhibitor, conserved site / Cereal trypsin/alpha-amylase inhibitors family signature. / Cereal seed allergen/grain softness/trypsin and alpha-amylase inhibitor / Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / 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 / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Alpha-amylase/trypsin inhibitor / Alpha-amylase
Similarity search - Component
Biological speciesTenebrio molitor (yellow mealworm)
Eleusine coracana (finger millet)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGomis-Rueth, F.X. / Strobl, S. / Glockshuber, R.
Citation
Journal: Structure / Year: 1998
Title: A novel strategy for inhibition of alpha-amylases: yellow meal worm alpha-amylase in complex with the Ragi bifunctional inhibitor at 2.5 A resolution.
Authors: Strobl, S. / Maskos, K. / 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
DepositionJan 13, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ALPHA-AMYLASE)
B: PROTEIN (RAGI BIFUNCTIONAL INHIBITOR)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0544
Polymers63,9792
Non-polymers762
Water5,963331
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.160, 186.870, 111.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (ALPHA-AMYLASE)


Mass: 51263.066 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tenebrio molitor (yellow mealworm) / Tissue: LARVAE / References: UniProt: P56634, alpha-amylase
#2: Protein PROTEIN (RAGI BIFUNCTIONAL INHIBITOR)


Mass: 12715.823 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Eleusine coracana (finger millet) / Organ: SEED / References: UniProt: P01087
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ALPHA-AMYLASE N-TERMINUS BLOCKS AGAINST AMINOPEPTIDASE ACTIVITY BY GLUTAMINE CYCLIZATION TO ...THE ALPHA-AMYLASE N-TERMINUS BLOCKS AGAINST AMINOPEPTIDASE ACTIVITY BY GLUTAMINE CYCLIZATION 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: 3.22 Å3/Da / Density % sol: 61.83 %
Crystal growDetails: 200MM AMMONIUM PHOSPHATE, 100MM TRIS-HCL, PH 8.5, 50% (W/V) 2-METHYL-2,4- PENTANEDIOL
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mMsodium acetate1drop
20.1 mM1dropCaCl2
3100 mM1dropNaCl
430 mg/mlprotein1drop
5200 mMammonium phosphate1reservoir
6100 mMTris-HCl1reservoir
750 %(w/v)MPD1reservoir

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 28178 / % possible obs: 97.3 % / Observed criterion σ(I): 3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 5.5
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 2.5 / % possible all: 89.8
Reflection
*PLUS
Observed criterion σ(I): 3 / Num. measured all: 78106
Reflection shell
*PLUS
% possible obs: 89.8 %

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Processing

Software
NameVersionClassification
MOSFLMV. 5.30data reduction
CCP4data reduction
AMoREphasing
X-PLOR3.1refinement
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BIP

1bip


Resolution: 2.5→7 Å / Cross valid method: FREE R FACTOR / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.261 -7 %
Rwork0.191 --
obs0.191 26825 -
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4487 0 3 330 4820
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 7 Å / σ(F): 0 / % reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.563

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