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- PDB-6hgf: Crystal structure of Alpha1-antichymotrypsin variant NewBG-II: a ... -

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Basic information

Entry
Database: PDB / ID: 6hgf
TitleCrystal structure of Alpha1-antichymotrypsin variant NewBG-II: a new binding globulin in complex with cortisol
Components(Alpha-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 / 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 / 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
Chem-HCY / Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 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
Polymers46,5982
Non-polymers4873
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, the protein molecule consists of chains A and B
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-33 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.300, 75.580, 79.880
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 / ACT / Cell growth-inhibiting gene 24/25 protein / Serpin A3


Mass: 41849.449 Da / Num. of mol.: 1 / Mutation: L24R, E242Q, K244N, 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 / 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 SALVE and the very C-terminal alanine residue 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-HCY / (11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione / CORTISOL


Mass: 362.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, hormone*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.34 Å3/Da / Density % sol: 47.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium sulfate, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.65→34.16 Å / Num. obs: 52767 / % possible obs: 99 % / Redundancy: 4.1 % / CC1/2: 0.999 / Rrim(I) all: 0.063 / Net I/σ(I): 18.4
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.01 / Num. unique obs: 8272 / CC1/2: 0.828 / Rrim(I) all: 0.536 / % possible all: 97.5

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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: 6HGD

6hgd


Resolution: 1.651→34.16 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 17.37
RfactorNum. reflection% reflection
Rfree0.1873 2110 4 %
Rwork0.1574 --
obs0.1586 52767 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.651→34.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2970 0 34 482 3486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063204
X-RAY DIFFRACTIONf_angle_d0.7934364
X-RAY DIFFRACTIONf_dihedral_angle_d23.9521204
X-RAY DIFFRACTIONf_chiral_restr0.393510
X-RAY DIFFRACTIONf_plane_restr0.005549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.651-1.68940.2831350.21663249X-RAY DIFFRACTION96
1.6894-1.73170.24021370.20163295X-RAY DIFFRACTION98
1.7317-1.77850.22711390.18853321X-RAY DIFFRACTION99
1.7785-1.83080.22431380.17963326X-RAY DIFFRACTION99
1.8308-1.88990.20271390.1753333X-RAY DIFFRACTION99
1.8899-1.95750.22611390.16463324X-RAY DIFFRACTION99
1.9575-2.03580.19861400.1523361X-RAY DIFFRACTION99
2.0358-2.12850.17381390.15333348X-RAY DIFFRACTION99
2.1285-2.24070.19991410.14863379X-RAY DIFFRACTION99
2.2407-2.3810.20031410.15093378X-RAY DIFFRACTION100
2.381-2.56480.21411420.16053408X-RAY DIFFRACTION100
2.5648-2.82280.18871420.16043408X-RAY DIFFRACTION100
2.8228-3.2310.19941430.15843430X-RAY DIFFRACTION100
3.231-4.06970.15071450.13713487X-RAY DIFFRACTION100
4.0697-34.16750.14961500.15173610X-RAY DIFFRACTION100

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