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- PDB-1jxj: Role of mobile loop in the mechanism of human salivary amylase -

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Basic information

Entry
Database: PDB / ID: 1jxj
TitleRole of mobile loop in the mechanism of human salivary amylase
ComponentsAlpha-amylase, salivary
KeywordsHYDROLASE / amylase / mutagenesis / catalysis / human / salivary / enzyme / mobile loop
Function / homology
Function and homology information


Digestion of dietary carbohydrate / oligosaccharide metabolic process / alpha-amylase / alpha-amylase activity / chloride ion binding / carbohydrate metabolic process / calcium ion binding / extracellular space / extracellular exosome
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
Alpha-amylase 1B / Alpha-amylase 1C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsRamasubbu, N. / Ragunath, C. / Wang, Z. / Mishra, P.J. / Thomas, L.M.
CitationJournal: Eur.J.Biochem. / Year: 2004
Title: Human salivary alpha-amylase Trp58 situated at subsite -2 is critical for enzyme activity.
Authors: Ramasubbu, N. / Ragunath, C. / Mishra, P.J. / Thomas, L.M. / Kandra, L.
History
DepositionSep 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-amylase, salivary
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9583
Polymers55,8821
Non-polymers762
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.295, 75.250, 135.018
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Alpha-amylase, salivary / E.C.3.2.1.1 / salivary alpha-amyalse / 1 / 4-alpha-D-glucan glucanohydrolase


Mass: 55882.203 Da / Num. of mol.: 1 / Mutation: W58L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: salivary glands / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P04745, UniProt: P0DTE8*PLUS, 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.: 294 / 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: 2.24 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: MPD, calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 mg/mlprotein1drop
210 mMTris-HCl1drop
35 mM1dropCaCl2
440 %MPD1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 21, 2001 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.99→65.94 Å / Num. all: 36288 / Num. obs: 34452 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.051 / Net I/σ(I): 16.2
Reflection shellResolution: 1.99→2.07 Å / Rmerge(I) obs: 0.062 / Mean I/σ(I) obs: 3 / Rsym value: 0.281 / % possible all: 95
Reflection
*PLUS
Redundancy: 3.8 %
Reflection shell
*PLUS
% possible obs: 95 % / Rmerge(I) obs: 0.281

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1SMD

1smd


Resolution: 1.99→65.94 Å / Cor.coef. Fo:Fc: 0.959 / SU B: 3.4 / SU ML: 0 / SU Rfree: 0.1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.19835 1795 5 %RANDOM
Rwork0.16448 ---
all0.1661 34452 --
obs0.16615 34452 97.7 %-
Displacement parametersBiso mean: 22.987 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.142 Å0.165 Å
Refinement stepCycle: LAST / Resolution: 1.99→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 2 294 4236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.01504058
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.95511
X-RAY DIFFRACTIONr_gen_planes_refined0.00703226
X-RAY DIFFRACTIONr_nbtor_refined0.00703226
X-RAY DIFFRACTIONr_chiral_restr0.1290.2554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8263495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.1290.2554
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.32028
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1230.5471
X-RAY DIFFRACTIONr_mcbond_it0.7981.52452
X-RAY DIFFRACTIONr_mcangle_it1.41223940
X-RAY DIFFRACTIONr_scbond_it2.29931606
X-RAY DIFFRACTIONr_scangle_it3.4194.51571
LS refinement shellResolution: 1.995→2.047 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.264 118
Rwork0.216 -
obs-2375
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.6
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.264 / Rfactor Rwork: 0.216

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