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- PDB-1pif: PIG ALPHA-AMYLASE -

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Basic information

Entry
Database: PDB / ID: 1pif
TitlePIG ALPHA-AMYLASE
ComponentsALPHA-AMYLASE
KeywordsGLYCOSYLTRANSFERASE / ALPHA-AMYLASE ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE GLYCOSYLTRANSFERASE
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate catabolic process / chloride ion binding / carbohydrate metabolic process / calcium ion binding / extracellular space
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
Pancreatic alpha-amylase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / PATTERSON SEARCH / Resolution: 2.3 Å
AuthorsMachius, M. / Vertesy, L. / Huber, R. / Wiegand, G.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Carbohydrate and protein-based inhibitors of porcine pancreatic alpha-amylase: structure analysis and comparison of their binding characteristics.
Authors: Machius, M. / Vertesy, L. / Huber, R. / Wiegand, G.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: The Crystal Structure of Porcine Pancreatic Alpha-Amylase in Complex with the Microbial Inhibitor Tendamistat
Authors: Wiegand, G. / Epp, O. / Huber, R.
#2: Journal: Protein Sci. / Year: 1995
Title: Carbohydrate Binding Sites in a Pancreatic Alpha-Amylase-Substrate Complex, Derived from X-Ray Structure Analysis at 2.1 Angstrom Resolution
Authors: Qian, M. / Haser, R. / Payan, F.
#3: Journal: J.Mol.Biol. / Year: 1994
Title: Refined Molecular Structure of Pig Pancreatic Alpha-Amylase at 2.1 A Resolution
Authors: Larson, S.B. / Greenwood, A. / Cascio, D. / Day, J. / McPherson, A.
#4: Journal: Biochemistry / Year: 1994
Title: The Active Center of a Mammalian Alpha-Amylase. Structure of the Complex of a Pancreatic Alpha-Amylase with a Carbohydrate Inhibitor Refined to 2.2-A Resolution
Authors: Qian, M. / Haser, R. / Buisson, G. / Duee, E. / Payan, F.
#5: Journal: J.Mol.Biol. / Year: 1993
Title: Structure and Molecular Model Refinement of Pig Pancreatic Alpha-Amylase at 2.1 A Resolution
Authors: Qian, M. / Haser, R. / Payan, F.
History
DepositionJun 15, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: 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: Database references / Derived calculations / Refinement description
Category: pdbx_struct_conn_angle / software ...pdbx_struct_conn_angle / software / struct_conn / struct_ref_seq_dif
Item: _software.name / _struct_ref_seq_dif.details
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: 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 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-AMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4493
Polymers55,3741
Non-polymers762
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.700, 114.900, 118.900
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 / ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE


Mass: 55373.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: PANCREAS / References: UniProt: P00690, 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.: 278 / Source method: isolated from a natural source / Formula: H2O
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: 4.39 Å3/Da / Density % sol: 72 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mg/mlprotein1drop
20.01 Mcacodylate1drop
30.02 M1dropCaCl2
41dropNH4OH

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Data collection

DiffractionMean temperature: 275 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 14, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→22.3 Å / Num. obs: 41481 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.082
Reflection shellResolution: 2.3→2.4 Å / % possible all: 81.5
Reflection shell
*PLUS
% possible obs: 81.5 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATA/AGROVATAdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: PATTERSON SEARCH
Starting model: PIG PANCREAS ALPHA-AMYLASE (REFERENCE 1)

Resolution: 2.3→7 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.208 -9.6 %
Rwork0.171 --
obs0.171 40433 94.7 %
Displacement parametersBiso mean: 32.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 10 278 4184
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.3→2.4 Å
RfactorNum. reflection% reflection
Rfree0.344 -9.6 %
Rwork0.319 3782 -
obs--81.5 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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