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- PDB-3sto: Serpin from the trematode Schistosoma Haematobium -

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Basic information

Entry
Database: PDB / ID: 3sto
TitleSerpin from the trematode Schistosoma Haematobium
ComponentsSerine protease inhibitor
KeywordsHYDROLASE INHIBITOR / serpin fold / protease inhibitor
Function / homology
Function and homology information


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 superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / 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
Similarity search - Component
Biological speciesSchistosoma haematobium (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.41 Å
AuthorsGranzin, J. / Weiergraeber, O.H. / Lee, X. / Blanton, R.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Three-dimensional structure of a schistosome serpin revealing an unusual configuration of the helical subdomain.
Authors: Granzin, J. / Huang, Y. / Topbas, C. / Huang, W. / Wu, Z. / Misra, S. / Hazen, S.L. / Blanton, R.E. / Lee, X. / Weiergraber, O.H.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease inhibitor


Theoretical massNumber of molelcules
Total (without water)46,3501
Polymers46,3501
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.913, 64.913, 187.004
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Serine protease inhibitor


Mass: 46349.531 Da / Num. of mol.: 1 / Fragment: unp residues 2-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma haematobium (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q26502
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 50mM acetate buffer, 5% PEG 6000, 1% Triton X-100, 3% dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793, 0.9788, 0.9667
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 1999
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97881
30.96671
ReflectionResolution: 2.41→21.58 Å / Num. all: 18500 / Num. obs: 18443 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.5 % / Biso Wilson estimate: 28.7 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 36.6
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 14 % / Mean I/σ(I) obs: 8.97 / Rsym value: 0.418 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDphasing
PHENIX(phenix.refine: 1.7_650)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.41→21.58 Å / SU ML: 0.26 / σ(F): 1.36 / Phase error: 19.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.213 936 5.1 %RANDOM
Rwork0.1624 ---
obs0.1649 18366 99.38 %-
all-18500 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.351 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso mean: 33.3 Å2
Baniso -1Baniso -2Baniso -3
1-5.8561 Å20 Å2-0 Å2
2--5.8561 Å2-0 Å2
3----11.7121 Å2
Refinement stepCycle: LAST / Resolution: 2.41→21.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2869 0 0 79 2948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132929
X-RAY DIFFRACTIONf_angle_d1.4173984
X-RAY DIFFRACTIONf_dihedral_angle_d15.8661041
X-RAY DIFFRACTIONf_chiral_restr0.083466
X-RAY DIFFRACTIONf_plane_restr0.006510
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.4053-2.53190.29271220.19342385275398
2.5319-2.69030.25741700.184924352605100
2.6903-2.89750.23871410.168924342575100
2.8975-3.18830.20631400.154724862626100
3.1883-3.64770.19271210.138125092630100
3.6477-4.58850.15241200.13425502670100
4.5885-21.58480.23761220.19212631275398

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