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- PDB-5om5: Crystal structure of Alpha1-antichymotrypsin variant DBS-I-allo1:... -

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Basic information

Entry
Database: PDB / ID: 5om5
TitleCrystal structure of Alpha1-antichymotrypsin variant DBS-I-allo1: an allosterically triggered drug-binding serpin for doxycycline
Components(Alpha-1-antichymotrypsin) x 2
KeywordsTRANSPORT PROTEIN / Serpin / alpha1-Antichymotrypsin / Doxycycline-binding protein / allosterically triggered drug release
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
Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.595 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 / 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)46,9396
Polymers46,7172
Non-polymers2224
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-41 kcal/mol
Surface area15530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.732, 84.732, 97.152
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 41972.488 Da / Num. of mol.: 1
Mutation: L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F A349R 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 K274S W276F R277F A349R 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.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 264 / 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: 42.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.0, 30 % v/v Jeffamine ED-2001 pH 7.0

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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: 1.595→42.4 Å / Num. obs: 53832 / % possible obs: 99.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 29.7 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.063 / Net I/σ(I): 18.5
Reflection shellResolution: 1.595→1.69 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 8352 / CC1/2: 0.751 / Rrim(I) all: 0.934 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.595→42.366 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.93
RfactorNum. reflection% reflection
Rfree0.1958 2100 3.9 %
Rwork0.1769 --
obs0.1777 53830 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.595→42.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 13 264 3247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093122
X-RAY DIFFRACTIONf_angle_d1.0214236
X-RAY DIFFRACTIONf_dihedral_angle_d21.4131175
X-RAY DIFFRACTIONf_chiral_restr0.239492
X-RAY DIFFRACTIONf_plane_restr0.005542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5951-1.63220.33021280.27933158X-RAY DIFFRACTION92
1.6322-1.6730.30391380.25983415X-RAY DIFFRACTION100
1.673-1.71830.28461390.23643423X-RAY DIFFRACTION100
1.7183-1.76880.24491400.21693432X-RAY DIFFRACTION100
1.7688-1.82590.23941390.20683431X-RAY DIFFRACTION100
1.8259-1.89120.22971390.19933418X-RAY DIFFRACTION100
1.8912-1.96690.22221410.19193468X-RAY DIFFRACTION100
1.9669-2.05640.18891390.17953429X-RAY DIFFRACTION100
2.0564-2.16490.21631400.183461X-RAY DIFFRACTION100
2.1649-2.30050.21021410.17683463X-RAY DIFFRACTION100
2.3005-2.47810.20531400.17593464X-RAY DIFFRACTION100
2.4781-2.72740.20571410.17923476X-RAY DIFFRACTION100
2.7274-3.1220.19311430.17723512X-RAY DIFFRACTION100
3.122-3.93290.17031430.15793515X-RAY DIFFRACTION100
3.9329-42.38090.15951490.15793665X-RAY DIFFRACTION100

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