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- PDB-4ro9: 2.0A resolution structure of SRPN2 (S358E) from Anopheles gambiae -

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Basic information

Entry
Database: PDB / ID: 4ro9
Title2.0A resolution structure of SRPN2 (S358E) from Anopheles gambiae
ComponentsSerpin 2
KeywordsHydrolase Inhibitor / serpin / serine protease inhibitor / insect immunity
Function / homology
Function and homology information


negative regulation of melanization defense response / negative regulation of endopeptidase activity / negative regulation of protein processing / defense response to protozoan / negative regulation of proteolysis / serine-type endopeptidase inhibitor activity / innate immune response / extracellular space
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
Serine protease inhibitor 2 / Serine protease inhibitor 2
Similarity search - Component
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLovell, S. / Battaile, K.P. / Zhang, X. / Meekins, D.A. / An, C. / Michel, K.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural and Inhibitory Effects of Hinge Loop Mutagenesis in Serpin-2 from the Malaria Vector Anopheles gambiae.
Authors: Zhang, X. / Meekins, D.A. / An, C. / Zolkiewski, M. / Battaile, K.P. / Kanost, M.R. / Lovell, S. / Michel, K.
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serpin 2
B: Serpin 2
C: Serpin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,3094
Polymers136,2173
Non-polymers921
Water4,486249
1
A: Serpin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4982
Polymers45,4061
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serpin 2


Theoretical massNumber of molelcules
Total (without water)45,4061
Polymers45,4061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Serpin 2


Theoretical massNumber of molelcules
Total (without water)45,4061
Polymers45,4061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)171.329, 42.264, 185.623
Angle α, β, γ (deg.)90.000, 116.940, 90.000
Int Tables number5
Space group name H-MI121
DetailsThere are 3 biological units in the asymmetric unit.

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Components

#1: Protein Serpin 2 /


Mass: 45405.629 Da / Num. of mol.: 3 / Mutation: S358E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Gene: SRPN2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pRare / References: UniProt: Q005N3, UniProt: Q7QIJ8*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.2 Å3/Da / Density % sol: 44.07 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 20% (w/v) PEG 3350, 100mM Bis-Tris Propane, 200 mM Sodium Malonate, pH 8.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→93.15 Å / Num. obs: 80845 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 32.17 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2-2.043.50.5692.115190439099.7
10.39-93.153.10.01952.7196163297.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.1.16data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PZF

3pzf


Resolution: 2→38.183 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.53 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 4050 5.01 %RANDOM
Rwork0.1903 ---
obs0.1927 80802 99.53 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.51 Å2 / Biso mean: 41.1477 Å2 / Biso min: 18.31 Å2
Refinement stepCycle: LAST / Resolution: 2→38.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8306 0 6 249 8561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098518
X-RAY DIFFRACTIONf_angle_d1.1511574
X-RAY DIFFRACTIONf_chiral_restr0.0681289
X-RAY DIFFRACTIONf_plane_restr0.0061514
X-RAY DIFFRACTIONf_dihedral_angle_d15.0243072
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02350.30971330.258326192752100
2.0235-2.04820.29321200.254526182738100
2.0482-2.07410.34571430.253626242767100
2.0741-2.10140.3281340.25412646278099
2.1014-2.13020.34361490.243126302779100
2.1302-2.16060.26681260.227225782704100
2.1606-2.19290.28631270.22122634276199
2.1929-2.22710.2851330.220127132846100
2.2271-2.26370.29921470.211125552702100
2.2637-2.30270.2671460.209126172763100
2.3027-2.34460.29571500.208126832833100
2.3446-2.38960.26351530.205725852738100
2.3896-2.43840.26591410.196726442785100
2.4384-2.49140.24911130.186826672780100
2.4914-2.54940.24661550.184325742729100
2.5494-2.61310.23631550.186326812836100
2.6131-2.68370.28551480.196626262774100
2.6837-2.76270.24541300.185126462776100
2.7627-2.85180.26061440.185926412785100
2.8518-2.95370.24351340.181826512785100
2.9537-3.07190.2541350.191726782813100
3.0719-3.21170.23651550.199726452800100
3.2117-3.38090.25581400.192226192759100
3.3809-3.59260.23861130.1892704281799
3.5926-3.86970.211440.17712669281399
3.8697-4.25870.20781260.16322681280799
4.2587-4.87390.17141350.15022647278298
4.8739-6.13640.19941580.18222695285399
6.1364-38.18970.23211630.20212782294599

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