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- PDB-6ftp: Crystal form 1 of Alpha1-antichymotrypsin variant DBS-II-allo: an... -

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Basic information

Entry
Database: PDB / ID: 6ftp
TitleCrystal form 1 of Alpha1-antichymotrypsin variant DBS-II-allo: an allosterically modulated drug-binding serpin for doxorubicin
Components(Alpha-1-antichymotrypsinAlpha 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 / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / collagen-containing extracellular matrix / secretory granule lumen / 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 / collagen-containing extracellular matrix / 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
DOXORUBICIN / Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionFeb 22, 2018Deposition 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 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _audit_author.name / _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)47,4376
Polymers46,7072
Non-polymers7304
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-23 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.240, 84.240, 97.443
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-527-

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: 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
Source method: isolated from a genetically manipulated source
Details: All N-terminal residues that are present in the sample sequence but not in the PDB file could not be modelled due to missing electron density. The protein is splitted into chain A and chain ...Details: All N-terminal residues that are present in the sample sequence but not in the PDB file could not be modelled due to missing electron density. The protein is splitted into chain A and chain B, as it belongs to the serine proteinase inhibitor (serpin) family and is proteolytically cleaved C-terminal of Gln360. The residues Gln360 and Arg376, which is the first residue visible in the electron density, are 70 angstrom apart because of the serpin-typical conformational change upon proteolytical cleavage. The sequence following the P1-P1' scissile bond, namely residues GPL..KQA, are part of chain B.
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: S361G A362P P382D T383N D384F Q386W N387S
Source method: isolated from a genetically manipulated source
Details: The protein is splitted into chain A and chain B, as it belongs to the serine proteinase inhibitor (serpin) family and is proteolytically cleaved C-terminal of Gln360. The residues Gln360 ...Details: The protein is splitted into chain A and chain B, as it belongs to the serine proteinase inhibitor (serpin) family and is proteolytically cleaved C-terminal of Gln360. The residues Gln360 and Arg376, which is the first residue visible in the electron density, are 70 angstrom apart because of the serpin-typical conformational change upon proteolytical cleavage. The sequence following the P1-P1' scissile bond, namely residues GPL..KQA, are part of chain B. The residues 361-366 (GPLVET) are missing in the PDB file because of 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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DM2 / DOXORUBICIN / ADRIAMYCIN / Doxorubicin


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


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium thiocyanate, 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: 1.8→42.12 Å / Num. obs: 37572 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 1 / Rrim(I) all: 0.061 / Rsym value: 0.058 / Net I/σ(I): 25.31
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 2.76 / Num. unique obs: 5991 / CC1/2: 0.854 / Rrim(I) all: 0.878 / Rsym value: 0.834 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OM8

5om8


Resolution: 1.8→42.12 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.34
RfactorNum. reflection% reflection
Rfree0.221 1877 5 %
Rwork0.1952 --
obs0.1965 37567 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→42.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2951 0 51 197 3199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013246
X-RAY DIFFRACTIONf_angle_d0.9394403
X-RAY DIFFRACTIONf_dihedral_angle_d19.4461186
X-RAY DIFFRACTIONf_chiral_restr0.229506
X-RAY DIFFRACTIONf_plane_restr0.006556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7994-1.84810.33311420.29942697X-RAY DIFFRACTION100
1.8481-1.90250.29151420.25682694X-RAY DIFFRACTION100
1.9025-1.96390.27071430.23072715X-RAY DIFFRACTION100
1.9639-2.03410.25171420.21812708X-RAY DIFFRACTION100
2.0341-2.11550.29311450.21742745X-RAY DIFFRACTION100
2.1155-2.21180.29591440.21672738X-RAY DIFFRACTION100
2.2118-2.32840.2781400.2052692X-RAY DIFFRACTION100
2.3284-2.47420.22381460.21012756X-RAY DIFFRACTION100
2.4742-2.66520.27151430.20952727X-RAY DIFFRACTION100
2.6652-2.93340.23221450.20542757X-RAY DIFFRACTION100
2.9334-3.35770.20981450.19452753X-RAY DIFFRACTION100
3.3577-4.22970.17621470.172800X-RAY DIFFRACTION100
4.2297-42.13150.17931530.17232908X-RAY DIFFRACTION100

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