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- PDB-3blp: Role of aromatic residues in human salivary alpha-amylase -

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Basic information

Entry
Database: PDB / ID: 3blp
TitleRole of aromatic residues in human salivary alpha-amylase
ComponentsAlpha-amylase 1AMY1A
KeywordsHYDROLASE / TIM Barrel / Greek Key barrel / Carbohydrate metabolism / Chloride / Glycoprotein / Glycosidase / Metal-binding / Pyrrolidone carboxylic acid / Secreted
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
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.
CitationJournal: Biologia / Year: 2008
Title: Structure-function relationships in human salivary alpha-amylase: role of aromatic residues in a secondary binding site
Authors: Ragunath, C. / Kasinathan, C. / Manuel, S.G.A. / Ramasubbu, N.
History
DepositionDec 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
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 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 3.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Alpha-amylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7426
Polymers55,8401
Non-polymers9025
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.085, 74.873, 134.690
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 / Sugars , 2 types, 3 molecules X

#1: Protein Alpha-amylase 1 / AMY1A / 1 / 4-alpha-D-glucan glucanohydrolase 1 / Salivary alpha-amylase


Mass: 55840.125 Da / Num. of mol.: 1 / Mutation: W388A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMY1A, AMY1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P04745, UniProt: P0DTE8*PLUS, alpha-amylase
#2: Polysaccharide 4-amino-4,6-dideoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 325.313 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DQuip[4N]a1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122m-1a_1-5_4*N]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 326 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-HMC / 5-HYDROXYMETHYL-CHONDURITOL / Valienol


Mass: 176.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H12O5
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 45% MPD, 0.1M Tris.HCl, 10 mM calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9777 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 18, 2007 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9777 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 67719 / Num. obs: 64253 / % possible obs: 96.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 20.6
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2 / Num. unique all: 3224 / Rsym value: 0.439 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SMD

1smd


Resolution: 1.6→30.96 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.545 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20532 3405 5 %RANDOM
Rwork0.18075 ---
all0.195 67719 --
obs0.18202 64253 96.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.671 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.42 Å20 Å2
3----0.66 Å2
Refine analyzeLuzzati coordinate error obs: 0.043 Å / Luzzati sigma a obs: 0.184 Å
Refinement stepCycle: LAST / Resolution: 1.6→30.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 56 323 4316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214113
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.9325589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.965495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69523.762210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27915622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9771528
X-RAY DIFFRACTIONr_chiral_restr0.0970.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023230
X-RAY DIFFRACTIONr_nbd_refined0.2050.21816
X-RAY DIFFRACTIONr_nbtor_refined0.3140.22813
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2270
X-RAY DIFFRACTIONr_metal_ion_refined0.0570.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.224
X-RAY DIFFRACTIONr_mcbond_it0.8221.52500
X-RAY DIFFRACTIONr_mcangle_it1.2923940
X-RAY DIFFRACTIONr_scbond_it1.98131865
X-RAY DIFFRACTIONr_scangle_it2.9174.51649
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 238 -
Rwork0.228 4500 -
obs--93.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.39490.06890.07870.39220.03650.29660.0178-0.0262-0.0014-0.0163-0.00290.00710.0096-0.019-0.0149-0.0477-0.0019-0.0022-0.07580.00020.09466.02158.03417.749
22.37550.03270.01540.4962-0.05030.56530.1177-0.0926-0.2753-0.0585-0.03070.03210.1879-0.0359-0.087-0.0207-0.0259-0.0403-0.11080.00340.13871.40634.95513.048
31.4519-0.14160.17860.7931-0.0021.22880.032-0.07270.1228-0.0104-0.008-0.0841-0.09830.0103-0.0241-0.0484-0.01390.0002-0.0944-0.02110.099321.80980.97727.073
418.30242.0703-4.8096.539-2.43091.82830.3484-0.3295-0.02750.2115-0.20940.04380.22710.4871-0.139-0.0137-0.0308-0.03290.0137-0.05740.02677.35943.66121.8
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X1 - 99
2X-RAY DIFFRACTION1X170 - 400
3X-RAY DIFFRACTION1X498
4X-RAY DIFFRACTION2X100 - 169
5X-RAY DIFFRACTION2X497
6X-RAY DIFFRACTION3X401 - 496
7X-RAY DIFFRACTION4X502 - 506

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