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- PDB-5om3: Crystal structure of Alpha1-antichymotrypsin variant DBS-I5: a MM... -

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Basic information

Entry
Database: PDB / ID: 5om3
TitleCrystal structure of Alpha1-antichymotrypsin variant DBS-I5: a MMP14-cleavable drug-binding serpin for doxycycline
Components(Alpha-1-antichymotrypsin) x 2
KeywordsTRANSPORT PROTEIN / Serpin / alpha1-Antichymotrypsin / Doxycycline-binding protein / MMP14-cleavable RCL
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 / extracellular space / DNA binding / 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 / DI(HYDROXYETHYL)ETHER / Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)47,2574
Polymers46,7062
Non-polymers5512
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-34 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.321, 84.321, 98.156
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-636-

HOH

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Components

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


Mass: 41827.348 Da / Num. of mol.: 1
Mutation: L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F V355L K356F T358P L360S S361L A362R L363M 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: 4878.847 Da / Num. of mol.: 1
Mutation: L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F V355L K356F T358P L360S S361L A362R L363M 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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→42.2 Å / Num. obs: 27859 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 35.6 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.0109 / Net I/σ(I): 15.6
Reflection shellResolution: 2→2.12 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4407 / CC1/2: 0.856 / Rrim(I) all: 0.908 / % possible all: 99.4

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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: 2→42.16 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.5
RfactorNum. reflection% reflection
Rfree0.2191 1392 5 %
Rwork0.1786 --
obs0.1806 27852 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→42.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 39 176 3148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083052
X-RAY DIFFRACTIONf_angle_d0.8614134
X-RAY DIFFRACTIONf_dihedral_angle_d10.6112532
X-RAY DIFFRACTIONf_chiral_restr0.053476
X-RAY DIFFRACTIONf_plane_restr0.005522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9965-2.06790.39121340.27122572X-RAY DIFFRACTION99
2.0679-2.15070.27141370.23582612X-RAY DIFFRACTION100
2.1507-2.24850.25071380.19792608X-RAY DIFFRACTION100
2.2485-2.36710.27191380.19192618X-RAY DIFFRACTION100
2.3671-2.51540.25111390.18682637X-RAY DIFFRACTION100
2.5154-2.70950.2371380.18842639X-RAY DIFFRACTION100
2.7095-2.98210.23261390.18562630X-RAY DIFFRACTION100
2.9821-3.41350.18151400.16962663X-RAY DIFFRACTION100
3.4135-4.30.18531410.15352684X-RAY DIFFRACTION100
4.3-42.16990.20081480.16632797X-RAY DIFFRACTION100

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