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- PDB-3ozq: Crystal structure of Serpin48, which is a highly specific serpin ... -

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Basic information

Entry
Database: PDB / ID: 3ozq
TitleCrystal structure of Serpin48, which is a highly specific serpin in the insect Tenebrio molitor
ComponentsSerpin48
KeywordsHYDROLASE INHIBITOR / Serpin / Serpin48 inhibits SPE specifically / SPE
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / 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
Biological speciesTenebrio molitor (yellow mealworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPark, S.H. / Piao, S. / Ha, N.-C.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and functional characterization of a highly specific serpin in the insect innate immunity
Authors: Park, S.H. / Jiang, R. / Piao, S. / Zhang, B. / Kim, E.H. / Kwon, H.M. / Jin, X.L. / Lee, B.L. / Ha, N.-C.
History
DepositionSep 27, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Mar 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serpin48


Theoretical massNumber of molelcules
Total (without water)42,2261
Polymers42,2261
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.061, 42.561, 66.178
Angle α, β, γ (deg.)90.00, 105.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serpin48


Mass: 42226.262 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 23-389
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tenebrio molitor (yellow mealworm) / Gene: SPN48 / Production host: Escherichia coli (E. coli) / References: UniProt: D1MYQ6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.13 Å3/Da / Density % sol: 42.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 13% PEG 8000, 0.11M Mes pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 10, 2010
RadiationMonochromator: Double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 28413 / Num. obs: 27674 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.3 Å2
Reflection shellResolution: 1.9→1.93 Å / % possible all: 89.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→29.22 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 221464.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2765 10 %RANDOM
Rwork0.221 ---
all0.227 28354 --
obs0.221 27617 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.1551 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 49.5 Å2
Baniso -1Baniso -2Baniso -3
1--15.06 Å20 Å20.98 Å2
2--16.39 Å20 Å2
3----1.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2891 0 0 105 2996
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.1
X-RAY DIFFRACTIONf_dihedral_angle_d25.4
X-RAY DIFFRACTIONf_improper_angle_d1.21
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.494 435 10 %
Rwork0.44 3929 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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