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- PDB-5om6: Crystal structure of Alpha1-antichymotrypsin variant DBS-I-allo2:... -

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Basic information

Entry
Database: PDB / ID: 5om6
TitleCrystal structure of Alpha1-antichymotrypsin variant DBS-I-allo2: a MMP9-cleavable drug-binding serpin for doxycycline
Components(Alpha-1-antichymotrypsin) x 2
KeywordsTRANSPORT PROTEIN / Serpin / alpha1-Antichymotrypsin / Doxycycline-binding protein / MMP9-cleavable RCL
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
CITRIC ACID / Alpha-1-antichymotrypsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
AuthorsSchmidt, K. / Muller, Y.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGRK-1962 Germany
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Design of an allosterically modulated doxycycline and doxorubicin drug-binding protein.
Authors: Schmidt, K. / Gardill, B.R. / Kern, A. / Kirchweger, P. / Borsch, M. / Muller, Y.A.
History
DepositionJul 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9189
Polymers93,3744
Non-polymers5445
Water6,738374
1
A: Alpha-1-antichymotrypsin
B: Alpha-1-antichymotrypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9414
Polymers46,6872
Non-polymers2542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Alpha-1-antichymotrypsin
D: Alpha-1-antichymotrypsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9775
Polymers46,6872
Non-polymers2903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.803, 73.921, 78.320
Angle α, β, γ (deg.)90.00, 99.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ACBD

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


Mass: 41924.457 Da / Num. of mol.: 2 / Fragment: UNP residues 36-383
Mutation: L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F A349R V355L I357G T358P L359R L360Q
Source method: isolated from a genetically manipulated source
Details: 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. C-terminal residues (ITA...KQA) are in chain I and K
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 / ACT / Cell growth-inhibiting gene 24/25 protein / Serpin A3


Mass: 4762.639 Da / Num. of mol.: 2 / Fragment: UNP residues 384-423
Mutation: L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F A349R V355L I357G T358P L359R L360Q
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 4 types, 379 molecules

#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M citric acid pH 3.5, 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.849→38.601 Å / Num. obs: 72070 / % possible obs: 98.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 33.2 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.068 / Net I/σ(I): 15.2
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 11566 / CC1/2: 0.766 / Rrim(I) all: 0.748 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.849→38.601 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.61
RfactorNum. reflection% reflection
Rfree0.2383 2100 2.92 %
Rwork0.1941 --
obs0.1954 72026 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.849→38.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6012 0 35 374 6421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086194
X-RAY DIFFRACTIONf_angle_d0.8298368
X-RAY DIFFRACTIONf_dihedral_angle_d20.8222302
X-RAY DIFFRACTIONf_chiral_restr0.057957
X-RAY DIFFRACTIONf_plane_restr0.0051072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8491-1.89220.35541370.354573X-RAY DIFFRACTION98
1.8922-1.93950.33071400.29614644X-RAY DIFFRACTION99
1.9395-1.99190.30861390.25614630X-RAY DIFFRACTION98
1.9919-2.05050.29061370.23994573X-RAY DIFFRACTION98
2.0505-2.11670.27621410.22394704X-RAY DIFFRACTION99
2.1167-2.19230.25151390.224632X-RAY DIFFRACTION99
2.1923-2.28010.26311410.20934678X-RAY DIFFRACTION99
2.2801-2.38390.25711410.20674697X-RAY DIFFRACTION100
2.3839-2.50950.27051390.20994635X-RAY DIFFRACTION98
2.5095-2.66670.29721380.21064591X-RAY DIFFRACTION97
2.6667-2.87260.22091400.20634686X-RAY DIFFRACTION100
2.8726-3.16150.27961430.19854744X-RAY DIFFRACTION100
3.1615-3.61870.21531400.18084673X-RAY DIFFRACTION99
3.6187-4.5580.17351410.15054693X-RAY DIFFRACTION99
4.558-38.60970.21511440.16144773X-RAY DIFFRACTION98

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