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- PDB-6hgn: Crystal structure of Alpha1-antichymotrypsin variant DBS-II-allo-... -

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Basic information

Entry
Database: PDB / ID: 6hgn
TitleCrystal structure of Alpha1-antichymotrypsin variant DBS-II-allo-L55V: an allosterically controlled doxorubicin-binding serpin with an unprecedentedly high ligand release efficacy
Components(Alpha-1-antichymotrypsin) x 2
KeywordsTRANSPORT PROTEIN / Serpin / alpha1-Antichymotrypsin / computational protein design / allosteric coupling
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
Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.478 Å
AuthorsSchmidt, K. / Muller, Y.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGRK-1962 Germany
CitationJournal: J.Struct.Biol. / Year: 2019
Title: NewBG: A surrogate corticosteroid-binding globulin with an unprecedentedly high ligand release efficacy.
Authors: Gardill, B.R. / Schmidt, K. / Muller, Y.A.
History
DepositionAug 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)46,9416
Polymers46,6932
Non-polymers2484
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-22 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.832, 84.832, 97.066
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, L55V, 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 residues that are present in the sample sequence but not in the PDB file could not be modelled due to missing electron density- residues following the sequence ..EVLFQ are part of ...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- residues following the sequence ..EVLFQ are part of chain B, as the protein is a family member of serine proteinase inhibitors (serpins) and proteolytically cleaved between EVLFQ-GPLV
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: 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
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 43.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2 % Tacsimate pH 4.0, 0.1 M Sodium acetate trihydrate pH 4.6, 16 % w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.478→42.416 Å / Num. obs: 67808 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rrim(I) all: 0.069 / Net I/σ(I): 18.5
Reflection shellResolution: 1.478→1.57 Å / Mean I/σ(I) obs: 1.92 / CC1/2: 0.864 / Rrim(I) all: 1.168

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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: 5OM7

5om7


Resolution: 1.478→42.416 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.86
RfactorNum. reflection% reflection
Rfree0.1988 2100 3.1 %
Rwork0.1791 --
obs0.1797 67851 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.478→42.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 16 260 3194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093117
X-RAY DIFFRACTIONf_angle_d1.0734230
X-RAY DIFFRACTIONf_dihedral_angle_d21.5361181
X-RAY DIFFRACTIONf_chiral_restr0.076492
X-RAY DIFFRACTIONf_plane_restr0.006540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4781-1.51250.29841360.28694286X-RAY DIFFRACTION99
1.5125-1.55030.26731380.25424314X-RAY DIFFRACTION100
1.5503-1.59220.30331390.24284355X-RAY DIFFRACTION100
1.5922-1.63910.24941390.22464331X-RAY DIFFRACTION100
1.6391-1.6920.25581390.22644356X-RAY DIFFRACTION100
1.692-1.75250.23281380.2174328X-RAY DIFFRACTION100
1.7525-1.82260.26431390.21264359X-RAY DIFFRACTION100
1.8226-1.90560.2231400.20274359X-RAY DIFFRACTION100
1.9056-2.00610.20651390.19544380X-RAY DIFFRACTION100
2.0061-2.13170.20661400.18564372X-RAY DIFFRACTION100
2.1317-2.29630.1841410.17964414X-RAY DIFFRACTION100
2.2963-2.52740.18661400.17054385X-RAY DIFFRACTION100
2.5274-2.8930.19351410.17254422X-RAY DIFFRACTION100
2.893-3.64460.18361420.16884455X-RAY DIFFRACTION100
3.6446-42.43350.18331490.15994635X-RAY DIFFRACTION100

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