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- PDB-1zyo: Crystal Structure of the Serine Protease Domain of Sesbania Mosai... -

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Basic information

Entry
Database: PDB / ID: 1zyo
TitleCrystal Structure of the Serine Protease Domain of Sesbania Mosaic Virus polyprotein
Componentsserine protease
KeywordsHYDROLASE / viral serine protease of trypsin fold / beta-barrel / glutamyl endopeptidase
Function / homology
Function and homology information


host cell membrane / viral translational frameshifting / serine-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
Peptidase S39 / Peptidase S39B, luteovirus / Peptidase family S39 domain profile. / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesSesbania mosaic virus
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.4 Å
AuthorsGayathri, P. / Satheshkumar, P.S. / Prasad, K. / Savithri, H.S. / Murthy, M.R.N.
CitationJournal: Virology / Year: 2006
Title: Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket
Authors: Gayathri, P. / Satheshkumar, P.S. / Prasad, K. / Nair, S. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionJun 10, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 9, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5222
Polymers20,4301
Non-polymers921
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.072, 74.072, 68.753
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-13-

HOH

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Components

#1: Protein serine protease


Mass: 20430.281 Da / Num. of mol.: 1 / Fragment: protease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sesbania mosaic virus / Genus: Sobemovirus / Gene: ORF2 / Plasmid: pRSET-C / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9EB08, glutamyl endopeptidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.5 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 8
Details: 0.2M Tris pH 8.0, 0.2M ammonium sulphate, 0.6M 1,6-hexane diol, 5mM mercaptoethanol, 4% glycerol, microbatch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 2, 2004 / Details: Osmic mirror
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 9999 / Num. obs: 9272 / % possible obs: 92.73 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.12 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 32.13
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.09 % / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 3.8 / Num. unique all: 554 / % possible all: 56.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0009refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.904 / SU B: 10.879 / SU ML: 0.251 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.503 / ESU R Free: 0.306
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28821 459 5.6 %RANDOM
Rwork0.2502 ---
all0.25234 9272 --
obs0.25234 7759 93.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.831 Å2
Baniso -1Baniso -2Baniso -3
1-2.78 Å21.39 Å20 Å2
2--2.78 Å20 Å2
3----4.16 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1346 0 6 45 1397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211385
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.9451885
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.655182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.14522.32643
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5315205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.767156
X-RAY DIFFRACTIONr_chiral_restr0.0790.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021020
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.2618
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2949
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5181.5924
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92421462
X-RAY DIFFRACTIONr_scbond_it0.993533
X-RAY DIFFRACTIONr_scangle_it1.6724.5423
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 30 -
Rwork0.351 402 -
obs--66.98 %

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