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- PDB-6z8l: Alpha-Amylase in complex with probe fragments -

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Basic information

Entry
Database: PDB / ID: 6z8l
TitleAlpha-Amylase in complex with probe fragments
ComponentsPancreatic alpha-amylase
KeywordsSUGAR BINDING PROTEIN / Alpha-Amylase / Complex / Maltose
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 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-maltose / alpha-D-glucopyranose / Pancreatic alpha-amylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.40000369636 Å
AuthorsAdam, S. / Koehnke, J.
Funding support1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KO 4116/3-1
CitationJournal: Chem Sci / Year: 2020
Title: Enhancing glycan stability via site-selective fluorination: modulating substrate orientation by molecular design.
Authors: Axer, A. / Jumde, R.P. / Adam, S. / Faust, A. / Schafers, M. / Fobker, M. / Koehnke, J. / Hirsch, A.K.H. / Gilmour, R.
History
DepositionJun 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)57,5888
Polymers55,9631
Non-polymers1,6257
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-20 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.873, 73.729, 135.207
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 55963.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P04746, alpha-amylase

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Sugars , 2 types, 5 molecules

#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: 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

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Non-polymers , 3 types, 368 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 60 % MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.4→48.431 Å / Num. obs: 102541 / % possible obs: 99.8 % / Redundancy: 6.3 % / Biso Wilson estimate: 17.3372979729 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.019 / Rrim(I) all: 0.047 / Net I/σ(I): 17.8
Reflection shellResolution: 1.4→1.48 Å / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 14829 / CC1/2: 0.81 / Rpim(I) all: 0.265 / Rrim(I) all: 0.672

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Processing

Software
NameVersionClassification
MolProbitymodel building
PHENIX1.11.1_2575refinement
MolProbitymodel building
MolProbitymodel building
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U3A

5u3a


Resolution: 1.40000369636→48.4309847473 Å / SU ML: 0.10702964517 / Cross valid method: FREE R-VALUE / σ(F): 1.33642473432 / Phase error: 14.9542321317
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.154231229896 5308 5.18116507887 %
Rwork0.141978268676 97140 -
obs0.142619864525 102448 99.6944395788 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.7573422784 Å2
Refinement stepCycle: LAST / Resolution: 1.40000369636→48.4309847473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3947 0 106 366 4419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01184248301814195
X-RAY DIFFRACTIONf_angle_d1.288163215075716
X-RAY DIFFRACTIONf_chiral_restr0.132532236143604
X-RAY DIFFRACTIONf_plane_restr0.00880695730527735
X-RAY DIFFRACTIONf_dihedral_angle_d15.08216151591486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.400004-1.41590.2577545555651760.228799116683154X-RAY DIFFRACTION99.8800239952
1.4159-1.43260.2475965627522040.2267372125383193X-RAY DIFFRACTION100
1.4326-1.450.2711874826491790.2153148509643232X-RAY DIFFRACTION99.9706916764
1.45-1.46840.219280157731390.2088892778093198X-RAY DIFFRACTION99.8802753667
1.4684-1.48770.2140232896891930.1937907533743201X-RAY DIFFRACTION99.9116867825
1.4877-1.50810.2171079731291740.1865125608223230X-RAY DIFFRACTION100
1.5081-1.52970.2007317695041690.1826509830943229X-RAY DIFFRACTION99.9411764706
1.5297-1.55250.2100385501351950.1764172047553171X-RAY DIFFRACTION99.8220640569
1.5525-1.57670.1801331633091810.1634086699863237X-RAY DIFFRACTION100
1.5767-1.60260.1693660657831570.16188696453200X-RAY DIFFRACTION100
1.6026-1.63020.1837955329731470.1601608953983254X-RAY DIFFRACTION99.7653270754
1.6302-1.65990.1750984022841660.1540385490523223X-RAY DIFFRACTION99.941020348
1.6599-1.69180.178081012561790.1558240638313203X-RAY DIFFRACTION100
1.6918-1.72630.1695339781071770.1529691668683235X-RAY DIFFRACTION99.8244587478
1.7263-1.76390.1719567434671740.1536543773833231X-RAY DIFFRACTION99.970640047
1.7639-1.80490.153786781991990.1441982942213225X-RAY DIFFRACTION99.9416228838
1.8049-1.85010.1477542725561700.1433218987293231X-RAY DIFFRACTION99.9706055262
1.8501-1.90010.1600760180141780.1458766330233210X-RAY DIFFRACTION99.9410029499
1.9001-1.9560.1619951279221600.137428522573266X-RAY DIFFRACTION99.9125109361
1.956-2.01910.1618970869671730.1352774736643219X-RAY DIFFRACTION99.7060552616
2.0191-2.09130.142656811322040.1354081507693235X-RAY DIFFRACTION99.9418773612
2.0913-2.1750.158581719181690.1287628400463244X-RAY DIFFRACTION99.8245100907
2.175-2.2740.1619528067511790.1262515790593254X-RAY DIFFRACTION99.7965116279
2.274-2.39390.1464653048061730.1240511419753245X-RAY DIFFRACTION99.5630643752
2.3939-2.54390.1367293018151780.1312060279633274X-RAY DIFFRACTION99.538638985
2.5439-2.74030.1419762758511520.1275140290563279X-RAY DIFFRACTION99.0187590188
2.7403-3.0160.1393460273061950.1245327531833252X-RAY DIFFRACTION99.2513676936
3.016-3.45230.1379969010611930.1297033838173279X-RAY DIFFRACTION99.2
3.4523-4.34910.1142497591351820.1184851902173306X-RAY DIFFRACTION98.6983588002
4.3491-48.430.169482819671930.1677934626193430X-RAY DIFFRACTION97.8924614969
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)
10.873410077736-0.1305270323710.100498552860.605191362646-0.07448608475580.6735040340220.0303275332143-0.0675303104112-0.1694609179720.07816022537160.0157968464534-0.01448497180040.1362942321640.0537425969291-0.04297747801220.1703310703630.0144585266547-0.02205668032230.1572357009530.01915090288450.150632269685-0.94674441031812.2301160609-11.2283937744
21.83479529183-0.6357405989770.6847992330381.77529481009-1.067224281412.628053914670.0205163576730.004954809296-0.103012932280.02041544073710.06761786576690.1982912740660.0742766599524-0.167913866325-0.1043220323810.105364864567-0.02917606029320.005626969469320.1469815085020.007601171375020.149830742287-21.372745059620.0448740507-20.5498329437
33.64911711993-1.90113891137-1.436871619882.153734536520.8210647972822.788347421480.06095266343810.260653453714-0.199405248743-0.096089724355-0.07899715888240.1091441355730.202984494932-0.07357721958560.03191092366530.103665032575-0.0175139513594-0.02139549291910.1215819593870.01278638640730.104131720213-10.782121017221.4483892791-28.8533543993
41.24976654194-0.480806340320.1245537579481.181570512180.007506072463420.5134178805810.003827081443640.1347299950410.15365382195-0.0343048509350.009327024371650.0622451975837-0.0820544838559-0.05990825121-0.01362739747490.139545803363-0.004809761577240.004659738590130.1829033953370.04715244717080.14250382541-13.972794356336.821415041-27.6669296465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 243 )
2X-RAY DIFFRACTION2chain 'A' and (resid 244 through 300 )
3X-RAY DIFFRACTION3chain 'A' and (resid 301 through 350 )
4X-RAY DIFFRACTION4chain 'A' and (resid 351 through 496 )

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