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

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Basic information

Entry
Database: PDB / ID: 6hgh
TitleCrystal structure of Alpha1-antichymotrypsin variant NewBG-III: a new binding globulin without any bound ligand
Components
  • Alpha-1-antichymotrypsin
  • alpha1-Antichymotrypsin
KeywordsTRANSPORT PROTEIN / Serpin / alpha1-Antichymotrypsin / computational protein design
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
MALONIC ACID / Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: alpha1-Antichymotrypsin
B: Alpha-1-antichymotrypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7503
Polymers46,6462
Non-polymers1041
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-41 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.160, 79.300, 102.200
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 alpha1-Antichymotrypsin


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) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Star / References: UniProt: P01011
#2: Protein/peptide 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-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 4 % Tacsimate pH 4.0, 12 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.9→38.183 Å / Num. obs: 31353 / % possible obs: 99.4 % / Redundancy: 3.64 % / CC1/2: 1 / Rrim(I) all: 0.041 / Net I/σ(I): 17.42
Reflection shellResolution: 1.9→2.02 Å / Mean I/σ(I) obs: 1.98 / CC1/2: 0.875 / Rrim(I) all: 0.748

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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: 6HGF

6hgf


Resolution: 1.9→38.183 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.87
RfactorNum. reflection% reflection
Rfree0.2405 2196 7 %
Rwork0.2075 --
obs0.2099 31360 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→38.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2905 0 7 109 3021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072976
X-RAY DIFFRACTIONf_angle_d0.8224034
X-RAY DIFFRACTIONf_dihedral_angle_d21.7661067
X-RAY DIFFRACTIONf_chiral_restr0.055470
X-RAY DIFFRACTIONf_plane_restr0.004512
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94130.38721360.36151808X-RAY DIFFRACTION100
1.9413-1.98650.38741350.33081788X-RAY DIFFRACTION99
1.9865-2.03620.33781330.291767X-RAY DIFFRACTION99
2.0362-2.09120.34471370.27661830X-RAY DIFFRACTION99
2.0912-2.15270.34211340.25911772X-RAY DIFFRACTION99
2.1527-2.22220.30211360.23071803X-RAY DIFFRACTION99
2.2222-2.30160.27441360.22481808X-RAY DIFFRACTION99
2.3016-2.39380.23871360.2041811X-RAY DIFFRACTION99
2.3938-2.50270.20891350.21991799X-RAY DIFFRACTION99
2.5027-2.63460.25121360.22551806X-RAY DIFFRACTION100
2.6346-2.79960.29881370.22861822X-RAY DIFFRACTION99
2.7996-3.01570.30391390.22531840X-RAY DIFFRACTION99
3.0157-3.3190.29221370.22921825X-RAY DIFFRACTION99
3.319-3.79890.21631400.20271857X-RAY DIFFRACTION100
3.7989-4.78480.20221410.16631876X-RAY DIFFRACTION100
4.7848-38.19040.18641480.18151952X-RAY DIFFRACTION98

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