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- PDB-6hgd: Crystal structure of Alpha1-antichymotrypsin variant NewBG-0: a n... -

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Basic information

Entry
Database: PDB / ID: 6hgd
TitleCrystal structure of Alpha1-antichymotrypsin variant NewBG-0: a new binding globulin variant that is devoid of any cortisol-binding capabilities
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 / secretory granule lumen / collagen-containing extracellular matrix / 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 / secretory granule lumen / collagen-containing extracellular matrix / 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
Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGardill, B.R. / Schmidt, K. / Muller, Y.A.
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


Theoretical massNumber of molelcules
Total (without water)46,6342
Polymers46,6342
Non-polymers00
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-38 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.550, 93.130, 49.330
Angle α, β, γ (deg.)90.00, 110.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 41858.469 Da / Num. of mol.: 1 / Mutation: L24R, E242Q, K244N, K274N, 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) / 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: 4775.638 Da / Num. of mol.: 1 / Mutation: P382D, T383H, D384F, Q386W
Source method: isolated from a genetically manipulated source
Details: the residues SAL 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 1.92 Å3/Da / Density % sol: 35.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride hexahydrate, 0.1 M BIS-Tris pH 6.5, 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.9→41.409 Å / Num. obs: 27559 / % possible obs: 99.2 % / Redundancy: 3.73 % / Rrim(I) all: 0.052 / Net I/σ(I): 20.56
Reflection shellResolution: 1.9→2.01 Å / Mean I/σ(I) obs: 7.86 / Rrim(I) all: 0.177

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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: 1AS4

1as4


Resolution: 1.9→38.939 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 19.23
RfactorNum. reflection% reflection
Rfree0.198 1379 5 %
Rwork0.1474 --
obs0.1499 27554 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→38.939 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2978 0 0 385 3363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073056
X-RAY DIFFRACTIONf_angle_d0.7984141
X-RAY DIFFRACTIONf_dihedral_angle_d19.9171127
X-RAY DIFFRACTIONf_chiral_restr0.384479
X-RAY DIFFRACTIONf_plane_restr0.005526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9004-1.96830.25121370.17412589X-RAY DIFFRACTION98
1.9683-2.04710.21741360.15632601X-RAY DIFFRACTION100
2.0471-2.14020.23011370.15512594X-RAY DIFFRACTION100
2.1402-2.25310.23451460.1542629X-RAY DIFFRACTION100
2.2531-2.39420.19581390.15082614X-RAY DIFFRACTION100
2.3942-2.5790.22481380.16272636X-RAY DIFFRACTION100
2.579-2.83850.19961350.15772599X-RAY DIFFRACTION100
2.8385-3.24910.19921350.15332643X-RAY DIFFRACTION100
3.2491-4.09280.17111350.132629X-RAY DIFFRACTION99
4.0928-38.94720.16951410.13312641X-RAY DIFFRACTION99

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