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- PDB-6hgm: Crystal structure of Alpha1-antichymotrypsin variant NewBG-III-al... -

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Basic information

Entry
Database: PDB / ID: 6hgm
TitleCrystal structure of Alpha1-antichymotrypsin variant NewBG-III-allo: an allosterically controlled new binding globulin with an unprecedentedly high ligand release efficacy
Components(Alpha-1-antichymotrypsin) x 2
KeywordsTRANSPORT PROTEIN / Serpin / alpha1-Antichymotrypsin / computational protein design / allosteric coupling
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
Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.369 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)47,08310
Polymers46,7322
Non-polymers3518
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-81 kcal/mol
Surface area15470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.338, 77.341, 79.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 41983.605 Da / Num. of mol.: 1
Mutation: L24R, L55V, E242Q, K244N, A251V, L252F, L269S, P270R, K274A, R277G, A349R
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 - residues following the sequence ..KITLL are part 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 - 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: 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

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Non-polymers , 4 types, 421 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 47.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.3 M calcium chloride dihydrate, 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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.369→38.671 Å / Num. obs: 91858 / % possible obs: 98.9 % / Redundancy: 4.44 % / CC1/2: 0.998 / Rrim(I) all: 0.067 / Net I/σ(I): 12.7
Reflection shellResolution: 1.37→1.45 Å / Mean I/σ(I) obs: 2.15 / CC1/2: 0.757 / Rrim(I) all: 0.702

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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: 1.369→38.67 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.77
RfactorNum. reflection% reflection
Rfree0.1812 2099 2.29 %
Rwork0.1682 --
obs0.1685 91853 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.369→38.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 0 14 413 3342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123146
X-RAY DIFFRACTIONf_angle_d1.2224287
X-RAY DIFFRACTIONf_dihedral_angle_d19.9481196
X-RAY DIFFRACTIONf_chiral_restr0.093498
X-RAY DIFFRACTIONf_plane_restr0.008544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3689-1.40070.28921350.27495781X-RAY DIFFRACTION97
1.4007-1.43570.24181360.25035823X-RAY DIFFRACTION98
1.4357-1.47460.23851390.22645925X-RAY DIFFRACTION99
1.4746-1.5180.21041400.21515983X-RAY DIFFRACTION99
1.518-1.5670.23181390.19865964X-RAY DIFFRACTION100
1.567-1.6230.21011390.18815946X-RAY DIFFRACTION99
1.623-1.68790.18851390.17955928X-RAY DIFFRACTION99
1.6879-1.76480.19041400.17525966X-RAY DIFFRACTION100
1.7648-1.85780.18471400.16546009X-RAY DIFFRACTION100
1.8578-1.97420.17991410.15826002X-RAY DIFFRACTION99
1.9742-2.12660.15191390.14945977X-RAY DIFFRACTION99
2.1266-2.34060.15751420.14666031X-RAY DIFFRACTION99
2.3406-2.67920.16751420.15436075X-RAY DIFFRACTION100
2.6792-3.37520.1551420.16066095X-RAY DIFFRACTION99
3.3752-38.68590.19111460.16416249X-RAY DIFFRACTION98

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