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- PDB-4x9y: Wild-Type Human Pancreatic Alpha-Amylase at True Atomic Resolutio... -

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Basic information

Entry
Database: PDB / ID: 4x9y
TitleWild-Type Human Pancreatic Alpha-Amylase at True Atomic Resolution (1.07 A)
ComponentsPancreatic alpha-amylase
KeywordsHYDROLASE / Amylase / atomic resolution / diabetes / glucosyl hydrolase / obesity
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: 1.07 Å
AuthorsCaner, S. / Brayer, G.D.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: To be published
Title: Wild-Type Human Pancreatic Alpha-Amylase at True Atomic Resolution (1.07 A)
Authors: Caner, S. / Brayer, G.D.
History
DepositionDec 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Aug 23, 2017Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen ...diffrn_detector / entity_src_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / software
Item: _diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_detector.detector / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.version
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jan 8, 2020Group: Author supporting evidence / Polymer sequence / Category: entity_poly / pdbx_audit_support
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 2.1Sep 27, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pancreatic alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0073
Polymers55,9311
Non-polymers762
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.200, 67.750, 130.230
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 / Fragment: UNP residues 16-511
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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


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


Mass: 18.015 Da / Num. of mol.: 527 / 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: 40.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 58% MPD, 100 mM sodium cacodylate, Quercitrin was added to saturating conditions into the crystal droplet.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.07→35 Å / Num. obs: 196249 / % possible obs: 96.5 % / Redundancy: 4.76 % / Rmerge(I) obs: 0.048 / Rsym value: 0.05 / Net I/σ(I): 16.18
Reflection shellResolution: 1.07→1.1 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.82 / % possible all: 71.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HNY

1hny


Resolution: 1.07→30.052 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 10.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1319 9813 5 %random selection
Rwork0.1126 ---
obs0.1136 196247 96.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.07→30.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3946 0 2 527 4475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074101
X-RAY DIFFRACTIONf_angle_d1.285570
X-RAY DIFFRACTIONf_dihedral_angle_d11.9551462
X-RAY DIFFRACTIONf_chiral_restr0.082560
X-RAY DIFFRACTIONf_plane_restr0.008740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.07-1.08220.23742230.23124228X-RAY DIFFRACTION66
1.0822-1.09490.22522460.20944690X-RAY DIFFRACTION74
1.0949-1.10830.21582800.19215302X-RAY DIFFRACTION83
1.1083-1.12230.18322990.175688X-RAY DIFFRACTION89
1.1223-1.13710.17383150.15765990X-RAY DIFFRACTION94
1.1371-1.15270.17273280.14326220X-RAY DIFFRACTION97
1.1527-1.16910.15843320.12626326X-RAY DIFFRACTION99
1.1691-1.18660.14353350.11676348X-RAY DIFFRACTION99
1.1866-1.20510.13393340.10656355X-RAY DIFFRACTION100
1.2051-1.22490.12553330.10416331X-RAY DIFFRACTION100
1.2249-1.2460.12083380.1026407X-RAY DIFFRACTION100
1.246-1.26870.11943340.09816363X-RAY DIFFRACTION100
1.2687-1.29310.11693360.10046385X-RAY DIFFRACTION100
1.2931-1.31940.11963370.09856396X-RAY DIFFRACTION100
1.3194-1.34810.11533360.09436383X-RAY DIFFRACTION100
1.3481-1.37950.12143380.09226431X-RAY DIFFRACTION100
1.3795-1.4140.11393380.09016413X-RAY DIFFRACTION100
1.414-1.45220.10983360.08756393X-RAY DIFFRACTION100
1.4522-1.4950.1063360.08646382X-RAY DIFFRACTION100
1.495-1.54320.10253390.08886431X-RAY DIFFRACTION100
1.5432-1.59840.1163360.08866393X-RAY DIFFRACTION100
1.5984-1.66240.10523390.09126428X-RAY DIFFRACTION100
1.6624-1.7380.11363400.09576459X-RAY DIFFRACTION100
1.738-1.82960.11353380.09986421X-RAY DIFFRACTION100
1.8296-1.94420.11623410.10296477X-RAY DIFFRACTION100
1.9442-2.09430.12053400.10526463X-RAY DIFFRACTION100
2.0943-2.3050.12323400.10366474X-RAY DIFFRACTION100
2.305-2.63840.13693420.11556486X-RAY DIFFRACTION99
2.6384-3.32340.14433460.12246571X-RAY DIFFRACTION100
3.3234-30.06340.15023580.13146800X-RAY DIFFRACTION99

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