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- PDB-5om7: Crystal structure of Alpha1-antichymotrypsin variant DBS-II: a dr... -

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Basic information

Entry
Database: PDB / ID: 5om7
TitleCrystal structure of Alpha1-antichymotrypsin variant DBS-II: a drug-binding serpin for doxorubicin
Components(Alpha-1-antichymotrypsinAlpha 1-antichymotrypsin) x 2
KeywordsTRANSPORT PROTEIN / Serpin / Alpha1-antichymotrypsin / Doxorubicin-binding protein / protein design
Function / homology
Function and homology information


maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / secretory granule lumen / collagen-containing extracellular matrix / blood microparticle ...maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / secretory granule lumen / collagen-containing extracellular matrix / blood microparticle / inflammatory response / Neutrophil degranulation / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DOXORUBICIN / Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.727 Å
AuthorsSchmidt, K. / Kern, A. / Muller, Y.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGRK-1962 Germany
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Design of an allosterically modulated doxycycline and doxorubicin drug-binding protein.
Authors: Schmidt, K. / Gardill, B.R. / Kern, A. / Kirchweger, P. / Borsch, M. / Muller, Y.A.
History
DepositionJul 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 2.0Jun 6, 2018Group: Atomic model / Data collection / Database references / Category: atom_site / citation
Item: _atom_site.occupancy / _citation.journal_volume ..._atom_site.occupancy / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Alpha-1-antichymotrypsin
B: Alpha-1-antichymotrypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1643
Polymers46,6212
Non-polymers5441
Water4,666259
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.463, 84.463, 98.322
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-689-

HOH

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Components

#1: Protein Alpha-1-antichymotrypsin / Alpha 1-antichymotrypsin / ACT / Cell growth-inhibiting gene 24/25 protein / Serpin A3


Mass: 41900.398 Da / Num. of mol.: 1
Mutation: L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F D278E V355L K356E I357V T358L L359F L360Q S361G A362P P382D T383N D384F Q386W N387S
Source method: isolated from a genetically manipulated source
Details: all residues that are present in the sample sequence but not in the PDB file could not be modelled due to missing electron density
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA3, AACT, GIG24, GIG25 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P01011
#2: Protein/peptide Alpha-1-antichymotrypsin / Alpha 1-antichymotrypsin / ACT / Cell growth-inhibiting gene 24/25 protein / Serpin A3


Mass: 4720.580 Da / Num. of mol.: 1
Mutation: L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F D278E V355L K356E I357V T358L L359F L360Q S361G A362P P382D T383N D384F Q386W N387S
Source method: isolated from a genetically manipulated source
Details: all residues that are present in the sample sequence but not in the PDB file could not be modelled due to missing electron density
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA3, AACT, GIG24, GIG25 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P01011
#3: Chemical ChemComp-DM2 / DOXORUBICIN / ADRIAMYCIN / Doxorubicin


Mass: 543.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29NO11 / Comment: medication, chemotherapy*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 43.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium chloride, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.73→42.231 Å / Num. obs: 42863 / % possible obs: 99.6 % / Redundancy: 8.2 % / Biso Wilson estimate: 34.8 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.066 / Net I/σ(I): 18.1
Reflection shellResolution: 1.73→1.83 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6786 / CC1/2: 0.893 / Rrim(I) all: 0.936 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.727→42.231 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.06
RfactorNum. reflection% reflection
Rfree0.2348 2100 4.9 %
Rwork0.1884 --
obs0.1907 42834 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.727→42.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2947 0 39 259 3245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143091
X-RAY DIFFRACTIONf_angle_d1.2684197
X-RAY DIFFRACTIONf_dihedral_angle_d21.6851134
X-RAY DIFFRACTIONf_chiral_restr0.077484
X-RAY DIFFRACTIONf_plane_restr0.008530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7274-1.76750.31881340.29092600X-RAY DIFFRACTION97
1.7675-1.81170.2771380.26882676X-RAY DIFFRACTION100
1.8117-1.86070.28271390.2432709X-RAY DIFFRACTION100
1.8607-1.91550.28681390.22592673X-RAY DIFFRACTION99
1.9155-1.97730.24121380.21822676X-RAY DIFFRACTION100
1.9773-2.0480.29811390.21492713X-RAY DIFFRACTION100
2.048-2.130.28621380.21522681X-RAY DIFFRACTION100
2.13-2.22690.25281400.20722708X-RAY DIFFRACTION100
2.2269-2.34430.25481400.19942711X-RAY DIFFRACTION100
2.3443-2.49120.23781400.19912714X-RAY DIFFRACTION100
2.4912-2.68350.28441390.20532704X-RAY DIFFRACTION100
2.6835-2.95350.24341410.20332746X-RAY DIFFRACTION100
2.9535-3.38070.2261420.18222754X-RAY DIFFRACTION100
3.3807-4.25870.19831430.162775X-RAY DIFFRACTION100
4.2587-42.24410.20131500.16192894X-RAY DIFFRACTION100

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