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- PDB-3lh4: Crystal Structure of Sialostatin L2 -

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Basic information

Entry
Database: PDB / ID: 3lh4
TitleCrystal Structure of Sialostatin L2
ComponentsSecreted cystatin
KeywordsHYDROLASE INHIBITOR / beta sheet / cystatin / Protease inhibitor / Thiol protease inhibitor
Function / homology
Function and homology information


cysteine-type endopeptidase inhibitor activity / vesicle / extracellular space / cytoplasm
Similarity search - Function
Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Salivary cystatin-L2
Similarity search - Component
Biological speciesIxodes scapularis (black-legged tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAndersen, J.F. / Kotsyfakis, M. / Salat, J. / Horka, H.
CitationJournal: Mol.Microbiol. / Year: 2010
Title: The crystal structures of two salivary cystatins from the tick Ixodes scapularis and the effect of these inhibitors on the establishment of Borrelia burgdorferi infection in a murine model.
Authors: Kotsyfakis, M. / Horka, H. / Salat, J. / Andersen, J.F.
History
DepositionJan 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Secreted cystatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9633
Polymers12,7751
Non-polymers1882
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.451, 95.451, 95.451
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

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Components

#1: Protein Secreted cystatin


Mass: 12775.076 Da / Num. of mol.: 1 / Fragment: UNP residues 19-132
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ixodes scapularis (black-legged tick) / Gene: IscW_ISCW018602 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: B7PKZ1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
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: 2.84 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.8 M Ammonium sulfate, 0.1 M Bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97902 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 21, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97902 Å / Relative weight: 1
ReflectionResolution: 1.8→19.48 Å / Num. all: 13472 / Num. obs: 13472 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 29.9 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 22.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 28 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 26.6 / Num. unique all: 1318 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.48 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.357 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19602 665 4.9 %RANDOM
Rwork0.17279 ---
all0.17391 13472 --
obs0.17391 12807 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.739 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms893 0 11 106 1010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021924
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9481256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3075116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.96924.88945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76315154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.861156
X-RAY DIFFRACTIONr_chiral_restr0.1030.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02694
X-RAY DIFFRACTIONr_mcbond_it0.7891.5574
X-RAY DIFFRACTIONr_mcangle_it1.4332925
X-RAY DIFFRACTIONr_scbond_it2.3543350
X-RAY DIFFRACTIONr_scangle_it4.0664.5330
LS refinement shellResolution: 1.804→1.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 54 -
Rwork0.172 939 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 32.2884 Å / Origin y: 24.2288 Å / Origin z: -1.2176 Å
111213212223313233
T0.0162 Å20.008 Å2-0.011 Å2-0.0573 Å20.0022 Å2--0.0465 Å2
L1.514 °2-1.2849 °20.491 °2-3.5508 °2-0.6845 °2--0.9937 °2
S-0.0298 Å °-0.0121 Å °-0.1487 Å °0.0289 Å °0.0861 Å °0.224 Å °0.0265 Å °-0.1601 Å °-0.0563 Å °

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