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- PDB-3mwz: Crystal structure of the selenomethionine derivative of the L 22,... -

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Basic information

Entry
Database: PDB / ID: 3mwz
TitleCrystal structure of the selenomethionine derivative of the L 22,47,100 M mutant of sialostatin L2
Componentssialostatin L2
KeywordsHYDROLASE INHIBITOR / antiparallel beta-sheet
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 / Salivary cystatin-L2
Similarity search - Component
Biological speciesIxodes scapularis (black-legged tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.52 Å
AuthorsAndersen, J.F.
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
DepositionMay 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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: sialostatin L2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1402
Polymers13,0441
Non-polymers961
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.267, 95.267, 95.267
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein sialostatin L2


Mass: 13043.797 Da / Num. of mol.: 1 / Fragment: residues 19-132 / Mutation: L40M, L65M, L118M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ixodes scapularis (black-legged tick) / Plasmid: pET 17b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: Q4PMS6, UniProt: B7PKZ1*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 9
Details: 1.8 M ammonium sulfate, 0.1 M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9712 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2008
Details: Rosenbaum-Rock double crystal monochromator Si(111)
RadiationMonochromator: Rosenbaum-Rock double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9712 Å / Relative weight: 1
ReflectionResolution: 1.52→67.42 Å / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.5
Reflection shellResolution: 1.52→1.57 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 6.9 / % possible all: 100

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.52→67.42 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.229 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20136 1135 5.1 %RANDOM
Rwork0.17432 ---
obs0.17568 21062 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.987 Å2
Refinement stepCycle: LAST / Resolution: 1.52→67.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms895 0 5 141 1041
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022920
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9361249
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3395116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82724.88945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03915158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.541156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02694
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6591.5574
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2562925
X-RAY DIFFRACTIONr_scbond_it1.983346
X-RAY DIFFRACTIONr_scangle_it3.1724.5323
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.52→1.561 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 80 -
Rwork0.213 1550 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 31.9499 Å / Origin y: 24.3754 Å / Origin z: -1.7461 Å
111213212223313233
T0.0283 Å20 Å20.0156 Å2-0.0329 Å2-0.0048 Å2--0.0492 Å2
L0.7749 °2-0.7179 °20.5398 °2-1.5878 °2-0.1948 °2--0.9897 °2
S0.0454 Å °-0.0232 Å °-0.082 Å °-0.0866 Å °-0.041 Å °0.103 Å °0.0712 Å °-0.1416 Å °-0.0044 Å °

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