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- PDB-3pzf: 1.75A resolution structure of Serpin-2 from Anopheles gambiae -

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Basic information

Entry
Database: PDB / ID: 3pzf
Title1.75A resolution structure of Serpin-2 from Anopheles gambiae
ComponentsSerpin 2
KeywordsHYDROLASE INHIBITOR / serpin / protease inhibitor / melanization
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: 1.75 Å
AuthorsLovell, S. / Battaile, K.P. / An, C. / Michel, K.
CitationJournal: Proteins / Year: 2011
Title: Crystal structure of native Anopheles gambiae serpin-2, a negative regulator of melanization in mosquitoes.
Authors: An, C. / Lovell, S. / Kanost, M.R. / Battaile, K.P. / Michel, K.
History
DepositionDec 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)45,3641
Polymers45,3641
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.538, 96.538, 78.289
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-559-

HOH

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Components

#1: Protein Serpin 2


Mass: 45363.594 Da / Num. of mol.: 1
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): BL-21 DE3 pRare / References: UniProt: Q005N3, UniProt: Q7QIJ8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 47.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 2.8 M Sodium Acetate, 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: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 6, 2010
Diffraction measurementDetails: 0.50 degrees, 0.5 sec, detector distance 124.99 mm
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.059 / Number: 41856
ReflectionResolution: 1.75→30 Å / Num. obs: 41856 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 35.946
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2.32 / Rsym value: 0.415 / % possible all: 78.7
Cell measurementReflection used: 41856

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å26.25 Å
Translation2.5 Å26.25 Å

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Processing

Software
NameVersionClassificationNB
PHENIXdev_605refinement
PHASER2.2.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Serpin-2 model from lower resolution data that was subsequently used for molecular replacement against this higher resolution data

Resolution: 1.75→26.254 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.19 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 2042 5.07 %RANDOM
Rwork0.1734 ---
all0.1751 40293 --
obs0.1751 40293 96.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.788 Å2 / ksol: 0.404 e/Å3
Displacement parametersBiso max: 106.1 Å2 / Biso mean: 35.6634 Å2 / Biso min: 14.39 Å2
Baniso -1Baniso -2Baniso -3
1--8.7167 Å20 Å20 Å2
2---8.7167 Å2-0 Å2
3---17.4334 Å2
Refinement stepCycle: LAST / Resolution: 1.75→26.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2931 0 0 165 3096
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg1.233
X-RAY DIFFRACTIONf_bond_d0.011
LS refinement shellResolution: 1.75→1.79 Å
RfactorNum. reflection% reflection
Rfree0.303 92 -
Rwork0.256 --
obs-1962 74 %
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)
11.35910.2033-0.37741.06270.13540.5820.0964-0.26010.35210.0249-0.04720.1359-0.0971-0.0058-0.02060.18480.00460.01480.24-0.00590.2159.51937.16637.7847
23.37290.1679-0.71511.2069-0.34040.753-0.15860.3542-0.4242-0.32540.1340.26610.1449-0.18320.00720.1882-0.032-0.01740.1935-0.01550.23735.877727.5939-3.047
33.18640.0624-0.1861.168-0.12910.28990.0103-0.1457-0.0258-0.0427-0.0011-0.14130.0006-0.0147-0.00590.15540.01180.00340.16670.01180.107224.84134.48451.8263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 27:85)A27 - 85
2X-RAY DIFFRACTION2(chain A and resid 86:208)A86 - 208
3X-RAY DIFFRACTION3(chain A and resid 209:409)A209 - 409

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