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- PDB-5om2: Crystal structure of Alpha1-antichymotrypsin variant DBS-I1: a dr... -

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Basic information

Entry
Database: PDB / ID: 5om2
TitleCrystal structure of Alpha1-antichymotrypsin variant DBS-I1: a drug-binding serpin for doxycycline
Components(Alpha-1-antichymotrypsin) x 2
KeywordsTRANSPORT PROTEIN / Serpin / alpha1-Antichymotrypsin / protein design / Doxycycline-binding protein
Function / homology
Function and homology information


maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / response to cytokine / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / : / secretory granule lumen ...maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / response to cytokine / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / : / secretory granule lumen / 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
Chem-DXT / Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsSchmidt, K. / 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 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: Alpha-1-antichymotrypsin
B: Alpha-1-antichymotrypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1214
Polymers46,6152
Non-polymers5072
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-35 kcal/mol
Surface area15320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.917, 84.917, 98.399
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-715-

HOH

21A-891-

HOH

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Components

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


Mass: 41870.371 Da / Num. of mol.: 1
Mutation: L24R W194F W215Y E242Q K244N L269S P270Q K274A W276F R277F V355L K356E I357V T358L L359F L360Q S361G A362P P382D T383H 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 / ACT / Cell growth-inhibiting gene 24/25 protein / Serpin A3


Mass: 4744.624 Da / Num. of mol.: 1
Mutation: L24R W194F W215Y E242Q K244N L269S P270Q K274A W276F R277F V355L K356E I357V T358L L359F L360Q S361G A362P P382D T383H 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DXT / (4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE / DOXYTETRACYCLINE / DOXYCYCLINE


Mass: 444.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24N2O8 / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.2 Å3/Da / Density % sol: 44.04 %
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: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.47→42.5 Å / Num. obs: 69528 / % possible obs: 99.1 % / Redundancy: 7.5 % / Biso Wilson estimate: 25.9 Å2 / CC1/2: 1 / Rrim(I) all: 0.059 / Net I/σ(I): 20.2
Reflection shellResolution: 1.47→1.56 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 10730 / CC1/2: 0.726 / Rrim(I) all: 0.992 / % possible all: 95.9

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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: 1.47→40.892 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.54
RfactorNum. reflection% reflection
Rfree0.2018 3474 5 %
Rwork0.1726 --
obs0.1741 69473 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.47→40.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 36 365 3343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013116
X-RAY DIFFRACTIONf_angle_d1.0634238
X-RAY DIFFRACTIONf_dihedral_angle_d20.5661160
X-RAY DIFFRACTIONf_chiral_restr0.25489
X-RAY DIFFRACTIONf_plane_restr0.006538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4698-1.490.25841230.28412348X-RAY DIFFRACTION89
1.49-1.51120.30921330.28512527X-RAY DIFFRACTION96
1.5112-1.53380.29591370.26182601X-RAY DIFFRACTION99
1.5338-1.55780.27571370.24082610X-RAY DIFFRACTION99
1.5578-1.58330.23911400.23592647X-RAY DIFFRACTION99
1.5833-1.61060.24531370.22842601X-RAY DIFFRACTION99
1.6106-1.63990.26721370.2212600X-RAY DIFFRACTION99
1.6399-1.67140.27731390.21882645X-RAY DIFFRACTION99
1.6714-1.70560.23031380.21452617X-RAY DIFFRACTION100
1.7056-1.74260.26841380.20582640X-RAY DIFFRACTION100
1.7426-1.78320.23971400.20242651X-RAY DIFFRACTION100
1.7832-1.82780.21861380.2072620X-RAY DIFFRACTION100
1.8278-1.87720.20351390.19412640X-RAY DIFFRACTION100
1.8772-1.93240.22381410.19932688X-RAY DIFFRACTION100
1.9324-1.99480.24471390.18512625X-RAY DIFFRACTION100
1.9948-2.06610.21241400.1812662X-RAY DIFFRACTION100
2.0661-2.14880.19791390.1752651X-RAY DIFFRACTION100
2.1488-2.24660.20971410.17032682X-RAY DIFFRACTION100
2.2466-2.3650.19491410.15942671X-RAY DIFFRACTION100
2.365-2.51320.19211400.15552659X-RAY DIFFRACTION100
2.5132-2.70720.17781410.16192687X-RAY DIFFRACTION100
2.7072-2.97960.17761420.16322685X-RAY DIFFRACTION100
2.9796-3.41050.1821430.15342732X-RAY DIFFRACTION100
3.4105-4.29620.16471440.14322721X-RAY DIFFRACTION100
4.2962-40.90790.19661470.15572789X-RAY DIFFRACTION98

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