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- PDB-4rsq: 2.9A resolution structure of SRPN2 (K198C/E359C) from Anopheles g... -

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Basic information

Entry
Database: PDB / ID: 4rsq
Title2.9A resolution structure of SRPN2 (K198C/E359C) from Anopheles gambiae
ComponentsSerpin 2
KeywordsHydrolase Inhibitor / serpin / serine protease / 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: 2.9 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
DepositionNov 10, 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serpin 2
B: Serpin 2
C: Serpin 2
D: Serpin 2
E: Serpin 2
F: Serpin 2
G: Serpin 2
H: Serpin 2
I: Serpin 2
J: Serpin 2
K: Serpin 2
L: Serpin 2


Theoretical massNumber of molelcules
Total (without water)543,73912
Polymers543,73912
Non-polymers00
Water00
1
A: Serpin 2


Theoretical massNumber of molelcules
Total (without water)45,3121
Polymers45,3121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Serpin 2


Theoretical massNumber of molelcules
Total (without water)45,3121
Polymers45,3121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Serpin 2


Theoretical massNumber of molelcules
Total (without water)45,3121
Polymers45,3121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Serpin 2


Theoretical massNumber of molelcules
Total (without water)45,3121
Polymers45,3121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Serpin 2


Theoretical massNumber of molelcules
Total (without water)45,3121
Polymers45,3121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Serpin 2


Theoretical massNumber of molelcules
Total (without water)45,3121
Polymers45,3121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Serpin 2


Theoretical massNumber of molelcules
Total (without water)45,3121
Polymers45,3121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Serpin 2


Theoretical massNumber of molelcules
Total (without water)45,3121
Polymers45,3121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Serpin 2


Theoretical massNumber of molelcules
Total (without water)45,3121
Polymers45,3121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Serpin 2


Theoretical massNumber of molelcules
Total (without water)45,3121
Polymers45,3121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: Serpin 2


Theoretical massNumber of molelcules
Total (without water)45,3121
Polymers45,3121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: Serpin 2


Theoretical massNumber of molelcules
Total (without water)45,3121
Polymers45,3121
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.925, 164.392, 186.181
Angle α, β, γ (deg.)90.000, 90.020, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThere are 12 biological units in the asymmetric unit.

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Components

#1: Protein
Serpin 2


Mass: 45311.582 Da / Num. of mol.: 12 / Mutation: K198C, E359C
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
Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.37 % / Mosaicity: 0.31 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.9
Details: 1.0 M sodium phosphate monobasic monohydrate, potassium phosphate dibasic, pH 6.9, 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: Oct 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.445
11h,-k,-l20.555
ReflectionResolution: 2.9→47.82 Å / Num. all: 129666 / Num. obs: 129666 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 7.9 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
2.9-2.953.30.63522087664170.41899.8
15.88-47.823.20.04518.625077740.03293.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.62
Highest resolutionLowest resolution
Rotation48.97 Å3.03 Å

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Processing

Software
NameVersionClassificationNB
Aimless0.3.11data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PZF

3pzf


Resolution: 2.9→47.82 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.886 / WRfactor Rfree: 0.2289 / WRfactor Rwork: 0.1733 / FOM work R set: 0.7541 / SU B: 11.965 / SU ML: 0.242 / SU Rfree: 0.0834 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2545 6285 4.8 %RANDOM
Rwork0.1939 ---
obs0.1968 129619 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 102.11 Å2 / Biso mean: 42.018 Å2 / Biso min: 16.9 Å2
Baniso -1Baniso -2Baniso -3
1--32.69 Å2-0 Å20.23 Å2
2--67.51 Å20 Å2
3----34.82 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33765 0 0 0 33765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01934534
X-RAY DIFFRACTIONr_bond_other_d0.0010.0231859
X-RAY DIFFRACTIONr_angle_refined_deg1.081.93946991
X-RAY DIFFRACTIONr_angle_other_deg0.71372834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20854209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.44125.3611746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.113155450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.73215112
X-RAY DIFFRACTIONr_chiral_restr0.0640.25266
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02140059
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028445
X-RAY DIFFRACTIONr_mcbond_it1.6194.35317007
X-RAY DIFFRACTIONr_mcbond_other1.6194.35317006
X-RAY DIFFRACTIONr_mcangle_it2.816.51621159
LS refinement shellResolution: 2.899→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 456 -
Rwork0.241 9002 -
all-9458 -
obs-1642 98.37 %

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