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- PDB-1jxk: Role of ethe mobile loop in the mehanism of human salivary amylase -

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Basic information

Entry
Database: PDB / ID: 1jxk
TitleRole of ethe mobile loop in the mehanism 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: 1.9 Å
AuthorsRamasubbu, N. / Ragunath, C. / Wang, Z.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Probing the role of a mobile loop in substrate binding and enzyme activity of human salivary amylase
Authors: Ramasubbu, N. / Ragunath, C. / Mishra, P.J.
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 2.1Aug 16, 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 / 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.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
Revision 2.2Nov 6, 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)55,7173
Polymers55,6421
Non-polymers762
Water5,819323
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.900, 75.737, 134.554
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: 55641.945 Da / Num. of mol.: 1 / Fragment: lacking the loop residues 306-310
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.: 323 / 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: 2.27 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: MPD, calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 mg/mlprotein1drop
210 mMTris-HCl1drop
35 mM1dropCaCl2
440 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 10, 2000 / 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: 1.9→67.42 Å / Num. all: 39061 / Num. obs: 38401 / % possible obs: 98.31 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 16.857 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 21.9
Reflection shellResolution: 1.9→1.949 Å / Rmerge(I) obs: 0.057 / Mean I/σ(I) obs: 8.6 / Rsym value: 0.155 / % possible all: 99
Reflection
*PLUS
Num. measured all: 174537

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Processing

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

1smd


Resolution: 1.9→67.42 Å / Cor.coef. Fo:Fc: 0.952 / SU B: 2.8 / SU ML: 0 / SU Rfree: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.1 / Stereochemistry target values: Engh & Huber / Details: MAXIMUM LIKELIHOOD RESTRAINED
RfactorNum. reflection% reflectionSelection details
Rfree0.19997 4300 10.1 %RANDOM
Rwork0.17346 ---
all0.1761 39061 --
obs0.17615 38401 98.31 %-
Displacement parametersBiso mean: 16.857 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.132 Å0.153 Å
Refinement stepCycle: LAST / Resolution: 1.9→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3923 0 2 323 4248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.00804043
X-RAY DIFFRACTIONr_angle_refined_deg1.321.95493
X-RAY DIFFRACTIONr_gen_planes_refined0.00503212
X-RAY DIFFRACTIONr_nbtor_refined0.00503212
X-RAY DIFFRACTIONr_chiral_restr0.0960.2551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2493490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79415662
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2150.32026
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1230.5426
X-RAY DIFFRACTIONr_mcbond_it0.5941.52429
X-RAY DIFFRACTIONr_mcangle_it1.12123910
X-RAY DIFFRACTIONr_scbond_it1.63531614
X-RAY DIFFRACTIONr_scangle_it2.5894.51583
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.244 327
Rwork0.196 -
obs-3162
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
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: 0.244 / Rfactor Rwork: 0.196

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