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- PDB-5u3a: Ultra High Resolution Crystal Structure of Human Pancreatic Alpha... -

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Basic information

Entry
Database: PDB / ID: 5u3a
TitleUltra High Resolution Crystal Structure of Human Pancreatic Alpha Amylase
ComponentsPancreatic alpha-amylase
KeywordsHYDROLASE / Amylase / Diabetes / Obesity / Glucosyl hydrolase
Function / homology
Function and homology information


polysaccharide digestion / Digestion of dietary carbohydrate / alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / chloride ion binding / carbohydrate metabolic process / calcium ion binding / extracellular space / extracellular exosome / extracellular region
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsCaner, S. / Brayer, G.D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institute of HealthCIHR MOP-111082 Canada
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Folding Then Binding vs Folding Through Binding in Macrocyclic Peptide Inhibitors of Human Pancreatic alpha-Amylase.
Authors: Goldbach, L. / Vermeulen, B.J.A. / Caner, S. / Liu, M. / Tysoe, C. / van Gijzel, L. / Yoshisada, R. / Trellet, M. / van Ingen, H. / Brayer, G.D. / Bonvin, A.M.J.J. / Jongkees, S.A.K.
History
DepositionDec 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Advisory / Data collection / Database references
Category: citation / citation_author / pdbx_database_PDB_obs_spr
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Polymer sequence / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_poly / 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 / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 27, 2022Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_database_PDB_obs_spr
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pancreatic alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2284
Polymers55,9311
Non-polymers2973
Water10,827601
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.100, 67.840, 130.410
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 Pancreatic alpha-amylase / PA / 1 / 4-alpha-D-glucan glucanohydrolase


Mass: 55931.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMY2A / Organ: Pancreas / Production host: Komagataella pastoris (fungus) / References: UniProt: P04746, alpha-amylase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 2.06 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: MPD 57%, 0.1 M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 0.95→40 Å / Num. obs: 267220 / % possible obs: 92.2 % / Redundancy: 6.8 % / CC1/2: 1 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.76
Reflection shellResolution: 0.95→0.97 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.88 / CC1/2: 0.71 / % possible all: 73.4

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.95→36.601 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 10.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1205 13358 5 %
Rwork0.1095 --
obs0.1101 267198 92.23 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.95→36.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3946 0 16 601 4563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084267
X-RAY DIFFRACTIONf_angle_d1.1215836
X-RAY DIFFRACTIONf_dihedral_angle_d14.4991564
X-RAY DIFFRACTIONf_chiral_restr0.097592
X-RAY DIFFRACTIONf_plane_restr0.009777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.96080.26513420.24596508X-RAY DIFFRACTION72
0.9608-0.97210.19673540.20746719X-RAY DIFFRACTION74
0.9721-0.9840.21173650.1986936X-RAY DIFFRACTION76
0.984-0.99640.22953690.18877009X-RAY DIFFRACTION77
0.9964-1.00950.18733770.16647163X-RAY DIFFRACTION79
1.0095-1.02340.15993900.15377408X-RAY DIFFRACTION81
1.0234-1.0380.16463930.1457484X-RAY DIFFRACTION83
1.038-1.05350.14544070.13727723X-RAY DIFFRACTION85
1.0535-1.070.1454160.12317906X-RAY DIFFRACTION87
1.07-1.08750.13094220.11468014X-RAY DIFFRACTION88
1.0875-1.10630.12564350.10688281X-RAY DIFFRACTION90
1.1063-1.12640.1144410.10098389X-RAY DIFFRACTION92
1.1264-1.1480.10194540.09848621X-RAY DIFFRACTION94
1.148-1.17150.10974630.09358800X-RAY DIFFRACTION96
1.1715-1.19690.10964710.09318933X-RAY DIFFRACTION98
1.1969-1.22480.11084780.09569092X-RAY DIFFRACTION99
1.2248-1.25540.114760.09319038X-RAY DIFFRACTION99
1.2554-1.28940.10544770.08719064X-RAY DIFFRACTION99
1.2894-1.32730.10154800.08629120X-RAY DIFFRACTION99
1.3273-1.37020.09574790.08619098X-RAY DIFFRACTION99
1.3702-1.41910.10264800.08999121X-RAY DIFFRACTION99
1.4191-1.47590.10134810.0879164X-RAY DIFFRACTION100
1.4759-1.54310.09544810.08689155X-RAY DIFFRACTION100
1.5431-1.62450.10184830.08719176X-RAY DIFFRACTION100
1.6245-1.72630.10684820.09349147X-RAY DIFFRACTION99
1.7263-1.85950.10664870.09839256X-RAY DIFFRACTION100
1.8595-2.04670.10764860.10219226X-RAY DIFFRACTION100
2.0467-2.34280.12094880.10439273X-RAY DIFFRACTION99
2.3428-2.95140.12594940.11719387X-RAY DIFFRACTION100
2.9514-36.62790.13375070.12899629X-RAY DIFFRACTION99

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