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- PDB-6hgk: Crystal structure of Alpha1-antichymotrypsin variant NewBG-III: a... -

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Basic information

Entry
Database: PDB / ID: 6hgk
TitleCrystal structure of Alpha1-antichymotrypsin variant NewBG-III: a new binding globulin in complex with progesterone
Components(Alpha-1-antichymotrypsinAlpha 1-antichymotrypsin) x 2
KeywordsTRANSPORT PROTEIN / Serpin / alpha1-Antichymotrypsin / computational protein design
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
PROGESTERONE / Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.855 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

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)47,0855
Polymers46,6462
Non-polymers4393
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-31 kcal/mol
Surface area15490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.426, 77.701, 79.151
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 41897.488 Da / Num. of mol.: 1
Mutation: L24R, L55V, E242Q, K244N, A251V, L252F, L269S, P270R, K274A, R277G
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 - residues following the sequence ..KITLL are ...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 - residues following the sequence ..KITLL are part of chain B, as the protein is a family member of serine proteinase inhibitors (serpins) and proteolytically cleaved between KITLL-SALVE
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA3, AACT, GIG24, GIG25 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (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: 4748.613 Da / Num. of mol.: 1 / Mutation: P382D, T383H, D384F, Q386W, N387S
Source method: isolated from a genetically manipulated source
Details: the residues SALVET 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) / Strain (production host): Star / References: UniProt: P01011
#3: Chemical ChemComp-STR / PROGESTERONE / Progesterone


Mass: 314.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O2 / Comment: hormone*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2 % Tacsimate pH 6.0, 0.1 M BIS-Tris pH 6.5, 20 % 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: P13 (MX1) / Wavelength: 0.97731 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97731 Å / Relative weight: 1
ReflectionResolution: 1.855→43.326 Å / Num. obs: 36786 / % possible obs: 99.6 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rrim(I) all: 0.105 / Net I/σ(I): 17.31
Reflection shellResolution: 1.855→1.97 Å / Mean I/σ(I) obs: 1.9 / CC1/2: 0.808 / Rrim(I) all: 1.245

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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: 6HGG

6hgg


Resolution: 1.855→38.85 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.29
RfactorNum. reflection% reflection
Rfree0.2269 1840 5 %
Rwork0.1791 --
obs0.1815 36766 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.855→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 31 202 3203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083135
X-RAY DIFFRACTIONf_angle_d0.7924256
X-RAY DIFFRACTIONf_dihedral_angle_d22.0171154
X-RAY DIFFRACTIONf_chiral_restr0.455494
X-RAY DIFFRACTIONf_plane_restr0.004538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8548-1.9050.32761350.31352551X-RAY DIFFRACTION96
1.905-1.9610.25161390.24742640X-RAY DIFFRACTION100
1.961-2.02430.26691410.21432679X-RAY DIFFRACTION100
2.0243-2.09670.23751400.19612665X-RAY DIFFRACTION100
2.0967-2.18060.22341410.19352677X-RAY DIFFRACTION100
2.1806-2.27990.23561390.18272640X-RAY DIFFRACTION100
2.2799-2.40.2441410.18132683X-RAY DIFFRACTION100
2.4-2.55040.24371410.18862669X-RAY DIFFRACTION100
2.5504-2.74720.23871420.18432703X-RAY DIFFRACTION100
2.7472-3.02360.24211420.18782691X-RAY DIFFRACTION100
3.0236-3.46090.23751430.18142726X-RAY DIFFRACTION100
3.4609-4.35940.1911450.15152748X-RAY DIFFRACTION100
4.3594-38.8590.21051510.16452854X-RAY DIFFRACTION99

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