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- PDB-5om8: Crystal form 2 of Alpha1-antichymotrypsin variant DBS-II-allo: an... -

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Basic information

Entry
Database: PDB / ID: 5om8
TitleCrystal form 2 of Alpha1-antichymotrypsin variant DBS-II-allo: an allosterically modulated drug-binding serpin for doxorubicin
Components(Alpha-1-antichymotrypsin) x 2
KeywordsTRANSPORT PROTEIN / Serpin / alpha1-Antichymotrypsin / Doxorubicin-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 / 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
NICKEL (II) ION / Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Alpha-1-antichymotrypsin
B: Alpha-1-antichymotrypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8635
Polymers46,7072
Non-polymers1563
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: protein was purified on a NI-NTA column
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-54 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.542, 84.542, 97.519
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 41986.516 Da / Num. of mol.: 1
Mutation: L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F D278E A349R 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 / 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 A349R 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

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Non-polymers , 4 types, 151 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
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: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.2→40.6 Å / Num. obs: 20967 / % possible obs: 99.6 % / Redundancy: 8.8 % / Biso Wilson estimate: 37 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.193 / Net I/σ(I): 11.1
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3292 / CC1/2: 0.58 / Rrim(I) all: 1.048 / % possible all: 98.4

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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: 2.2→40.583 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.82
RfactorNum. reflection% reflection
Rfree0.2423 1045 5 %
Rwork0.1853 --
obs0.1882 20898 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→40.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 0 6 148 3103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083006
X-RAY DIFFRACTIONf_angle_d0.8854054
X-RAY DIFFRACTIONf_dihedral_angle_d8.9511821
X-RAY DIFFRACTIONf_chiral_restr0.052466
X-RAY DIFFRACTIONf_plane_restr0.006518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.3160.26841470.21642795X-RAY DIFFRACTION100
2.316-2.46110.28331460.22482791X-RAY DIFFRACTION100
2.4611-2.65110.30851470.23162792X-RAY DIFFRACTION100
2.6511-2.91780.25281490.19852817X-RAY DIFFRACTION100
2.9178-3.33990.22991490.18072831X-RAY DIFFRACTION100
3.3399-4.20720.2281500.16922859X-RAY DIFFRACTION100
4.2072-40.59020.22451570.16632968X-RAY DIFFRACTION100

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