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- PDB-4roa: 1.90A resolution structure of SRPN2 (S358W) from Anopheles gambiae -

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Basic information

Entry
Database: PDB / ID: 4roa
Title1.90A resolution structure of SRPN2 (S358W) 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: 1.9 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
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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serpin 2


Theoretical massNumber of molelcules
Total (without water)45,4631
Polymers45,4631
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.946, 96.946, 78.569
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
DetailsThere are 1 biological units in the asymmetric unit.

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Components

#1: Protein Serpin 2


Mass: 45462.727 Da / Num. of mol.: 1 / Mutation: S358W
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 47.53 % / Mosaicity: 0.12 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 60% (w/v) Tacsimate, pH 7.0, 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: 1.9→48.47 Å / Num. obs: 33155 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Biso Wilson estimate: 24.57 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 18.4 / Scaling rejects: 2628
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.9-1.948.90.7982.7189382132100
9.11-48.479.80.04172316632399.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.8 Å42 Å
Translation1.8 Å42 Å

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Processing

Software
NameVersionClassificationNB
Aimless0.2.8data scaling
PHASER2.5.1phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PZF

3pzf


Resolution: 1.9→39.285 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 25.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2095 1671 5.05 %RANDOM
Rwork0.1721 ---
obs0.1741 33072 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.17 Å2 / Biso mean: 40.4323 Å2 / Biso min: 15.49 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2857 0 0 107 2964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012944
X-RAY DIFFRACTIONf_angle_d0.9514017
X-RAY DIFFRACTIONf_chiral_restr0.057451
X-RAY DIFFRACTIONf_plane_restr0.007525
X-RAY DIFFRACTIONf_dihedral_angle_d13.5791035
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.95590.30791340.249826122746100
1.9559-2.01910.24671450.198925972742100
2.0191-2.09120.22411220.177225992721100
2.0912-2.17490.22451390.175226042743100
2.1749-2.27390.23231330.182526342767100
2.2739-2.39380.24281310.197226142745100
2.3938-2.54370.23161560.198325982754100
2.5437-2.74010.2321460.174325962742100
2.7401-3.01580.24551450.176626232768100
3.0158-3.45190.20791540.177226022756100
3.4519-4.34820.17221330.141426432776100
4.3482-39.29290.17071330.16132679281299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.06890.35610.34014.58660.11492.5751-0.1494-0.3846-0.11610.44820.17460.20190.1518-0.0342-0.0320.26360.06440.03740.19030.01890.18066.66681.3618.492
22.4387-0.3723-0.23563.9683-0.47231.5663-0.0472-0.4595-0.74040.73010.13140.4480.0409-0.2167-0.12340.35560.04110.02730.27110.05820.359614.896365.35379.7019
32.285-1.60271.0313.2584-0.6031.04690.11320.45250.059-0.0682-0.1236-0.54680.08080.3251-0.01150.23140.02170.03470.318-0.04860.289821.672676.5192-2.1139
42.3779-0.5197-0.05953.8718-0.17531.4465-0.0809-0.03190.00360.13440.06560.41450.0471-0.10520.00940.16150.00980.01790.17560.00040.1956-1.820492.24683.2505
52.4452-1.04890.05052.74330.15250.4356-0.1244-0.06280.14790.30070.1701-0.2190.04730.079-0.01580.23820.0167-0.04040.1943-0.04690.156313.336284.07494.5003
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 56 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 94 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 95 through 211 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 212 through 299 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 300 through 409 )A0

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