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- PDB-6hge: Crystal structure of Alpha1-antichymotrypsin variant NewBG-I in t... -

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Basic information

Entry
Database: PDB / ID: 6hge
TitleCrystal structure of Alpha1-antichymotrypsin variant NewBG-I in the uncleaved S-conformation
Components(Alpha-1-antichymotrypsin) x 4
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
Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
C: Alpha-1-antichymotrypsin
D: Alpha-1-antichymotrypsin


Theoretical massNumber of molelcules
Total (without water)187,7094
Polymers187,7094
Non-polymers00
Water1,04558
1
A: Alpha-1-antichymotrypsin


Theoretical massNumber of molelcules
Total (without water)46,8941
Polymers46,8941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-1-antichymotrypsin


Theoretical massNumber of molelcules
Total (without water)46,9481
Polymers46,9481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-1-antichymotrypsin


Theoretical massNumber of molelcules
Total (without water)46,8941
Polymers46,8941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha-1-antichymotrypsin


Theoretical massNumber of molelcules
Total (without water)46,9751
Polymers46,9751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.000, 124.710, 127.500
Angle α, β, γ (deg.)90.00, 90.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 46893.504 Da / Num. of mol.: 1
Mutation: L24R, E242Q, K244N, L269S, P270R, K274N, R277G, P382D, T383H, 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 - dimethyl-lysines (MLY) have been modelled instead 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 - dimethyl-lysines (MLY) have been modelled instead of lysines (LYS) when the electron density confirmed the success of the reductive methylation process of surface lysines
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 Alpha-1-antichymotrypsin / ACT / Cell growth-inhibiting gene 24/25 protein / Serpin A3


Mass: 46947.594 Da / Num. of mol.: 1
Mutation: L24R, E242Q, K244N, L269S, P270R, K274N, R277G, P382D, T383H, 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) / Strain (production host): Star / References: UniProt: P01011
#3: Protein Alpha-1-antichymotrypsin / ACT / Cell growth-inhibiting gene 24/25 protein / Serpin A3


Mass: 46893.504 Da / Num. of mol.: 1
Mutation: L24R, E242Q, K244N, L269S, P270R, K274N, R277G, P382D, T383H, 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) / Strain (production host): Star / References: UniProt: P01011
#4: Protein Alpha-1-antichymotrypsin / ACT / Cell growth-inhibiting gene 24/25 protein / Serpin A3


Mass: 46974.641 Da / Num. of mol.: 1
Mutation: L24R, E242Q, K244N, L269S, P270R, K274N, R277G, P382D, T383H, 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) / Strain (production host): Star / References: UniProt: P01011
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NaCl, 0.1 M Tris-HCl, pH 8.5, 25 % PEG 3350 supplemented with 10 % of a 0.5 M NaF solution, and additional 0.1 ul of a silver bullets bio reagent mixture consisting of thymidine, ...Details: 0.2 M NaCl, 0.1 M Tris-HCl, pH 8.5, 25 % PEG 3350 supplemented with 10 % of a 0.5 M NaF solution, and additional 0.1 ul of a silver bullets bio reagent mixture consisting of thymidine, adenosine 3,5-cyclic monophosphate sodium salt monohydrate, sarcosine, 4-aminobenzoic acid, acarbose, inosine, 0.02 M HEPES sodium pH 6.8

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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 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.8→34.538 Å / Num. obs: 43876 / % possible obs: 98.1 % / Redundancy: 3.86 % / Rrim(I) all: 0.091 / Net I/σ(I): 15.31
Reflection shellResolution: 2.8→2.97 Å / Mean I/σ(I) obs: 2.62 / Rrim(I) all: 0.581

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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: 1YXA

1yxa


Resolution: 2.8→34.538 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 27.33
RfactorNum. reflection% reflection
Rfree0.2624 4387 10 %
Rwork0.1844 --
obs0.192 43864 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→34.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11519 0 0 58 11577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911750
X-RAY DIFFRACTIONf_angle_d1.0415889
X-RAY DIFFRACTIONf_dihedral_angle_d25.3224319
X-RAY DIFFRACTIONf_chiral_restr0.0531838
X-RAY DIFFRACTIONf_plane_restr0.0052002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83180.39111300.27391164X-RAY DIFFRACTION87
2.8318-2.86510.31511440.24371302X-RAY DIFFRACTION98
2.8651-2.90.32851500.22891346X-RAY DIFFRACTION98
2.9-2.93670.33131430.23331285X-RAY DIFFRACTION99
2.9367-2.97530.3241450.2281309X-RAY DIFFRACTION98
2.9753-3.01610.35521460.2141311X-RAY DIFFRACTION98
3.0161-3.05910.29621500.22561352X-RAY DIFFRACTION98
3.0591-3.10480.32791420.22641276X-RAY DIFFRACTION98
3.1048-3.15330.33231450.22261303X-RAY DIFFRACTION99
3.1533-3.20490.29591490.22461344X-RAY DIFFRACTION99
3.2049-3.26010.34391450.22351310X-RAY DIFFRACTION98
3.2601-3.31940.3161440.21341289X-RAY DIFFRACTION98
3.3194-3.38320.29771490.20891339X-RAY DIFFRACTION98
3.3832-3.45220.28961470.2031325X-RAY DIFFRACTION99
3.4522-3.52720.26321430.18721291X-RAY DIFFRACTION98
3.5272-3.60910.26311490.19051335X-RAY DIFFRACTION99
3.6091-3.69930.30741450.18531313X-RAY DIFFRACTION99
3.6993-3.79920.25451470.18741320X-RAY DIFFRACTION99
3.7992-3.91080.26431460.17991314X-RAY DIFFRACTION98
3.9108-4.03690.281480.18191331X-RAY DIFFRACTION99
4.0369-4.18090.23511470.1711327X-RAY DIFFRACTION99
4.1809-4.3480.23781460.1581310X-RAY DIFFRACTION99
4.348-4.54550.20861480.15431335X-RAY DIFFRACTION99
4.5455-4.78460.22851470.1471318X-RAY DIFFRACTION99
4.7846-5.08340.22711470.1521326X-RAY DIFFRACTION99
5.0834-5.47450.23121480.16621329X-RAY DIFFRACTION99
5.4745-6.02280.24711470.16831327X-RAY DIFFRACTION99
6.0228-6.88830.2481500.18071347X-RAY DIFFRACTION99
6.8883-8.65590.21411490.17131345X-RAY DIFFRACTION99
8.6559-34.5410.20671510.16631354X-RAY DIFFRACTION98

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