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- PDB-1z32: Structure-function relationships in human salivary alpha-amylase:... -

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Basic information

Entry
Database: PDB / ID: 1z32
TitleStructure-function relationships in human salivary alpha-amylase: Role of aromatic residues
ComponentsSalivary alpha-amylase
KeywordsHYDROLASE / TIM Barrel
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
4-amino-4,6-dideoxy-alpha-D-glucopyranose / alpha-D-glucopyranose / 5-HYDROXYMETHYL-CHONDURITOL / Alpha-amylase 1B / Alpha-amylase 1C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRamasubbu, N. / Ragunath, C. / Sundar, K. / Mishra, P.J. / Gyemant, G. / Kandra, L.
CitationJournal: To be Published
Title: Structure-function relationships in human salivary alpha-amylase: Role of aromatic residues
Authors: Ramasubbu, N. / Ragunath, C. / Sundar, K. / Mishra, P.J. / Gyemant, G. / Kandra, L.
History
DepositionMar 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp / _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 2.0Dec 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.3Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN According to author, AGL has a missing oxygen due to lack of electron density

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Salivary alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5186
Polymers55,9231
Non-polymers5955
Water6,107339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.657, 73.513, 134.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules X

#1: Protein Salivary alpha-amylase / 1 / 4-alpha-D-glucan glucanohydrolase


Mass: 55923.281 Da / Num. of mol.: 1 / Mutation: Y151M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMY1A, AMY1 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P04745, UniProt: P0DTE8*PLUS, alpha-amylase

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Sugars , 2 types, 2 molecules

#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar ChemComp-AGL / 4-amino-4,6-dideoxy-alpha-D-glucopyranose / 4,6-DIDEOXY-4-AMINO-ALPHA-D-GLUCOSE / 4-amino-4-deoxy-alpha-D-quinovopyranose / 4-amino-4,6-dideoxy-alpha-D-glucose / 4-amino-4,6-dideoxy-D-glucose / 4-amino-4,6-dideoxy-glucose


Type: D-saccharide, alpha linking / Mass: 163.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13NO4
IdentifierTypeProgram
DQuip[4N]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-6-deoxy-Glcp4NIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 342 molecules

#4: Chemical ChemComp-HMC / 5-HYDROXYMETHYL-CHONDURITOL / Valienol


Mass: 176.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H12O5
#5: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 42.85 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 9 / Details: MPD 40%, pH 9.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.6→42 Å / Num. all: 59813 / Num. obs: 58813 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 29
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 8 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1smd

1smd


Resolution: 1.6→19.84 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.256 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 3140 5.1 %RANDOM
Rwork0.17144 ---
all0.1919 58813 --
obs0.1725 58813 90.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.396 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3942 0 34 339 4315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214095
X-RAY DIFFRACTIONr_angle_refined_deg1.1531.9215559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9655495
X-RAY DIFFRACTIONr_chiral_restr0.0870.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023233
X-RAY DIFFRACTIONr_nbd_refined0.1950.21905
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2273
X-RAY DIFFRACTIONr_metal_ion_refined0.0340.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.222
X-RAY DIFFRACTIONr_mcbond_it0.5431.52452
X-RAY DIFFRACTIONr_mcangle_it1.02423940
X-RAY DIFFRACTIONr_scbond_it1.57131643
X-RAY DIFFRACTIONr_scangle_it2.4814.51619
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.233 215
Rwork0.205 4381

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