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- PDB-3zxy: Structure of S218A mutant of the protease domain of PatA -

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Basic information

Entry
Database: PDB / ID: 3zxy
TitleStructure of S218A mutant of the protease domain of PatA
ComponentsSUBTILISIN-LIKE PROTEIN
KeywordsHYDROLASE
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
Peptidase S8A, PatG / PatG/PatA-like domain / PatG domain / PatG, C-terminal / PatG Domain / PatG C-terminal / Peptidase S8/S53 domain / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. ...Peptidase S8A, PatG / PatG/PatA-like domain / PatG domain / PatG, C-terminal / PatG Domain / PatG C-terminal / Peptidase S8/S53 domain / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Subtilisin-like protein
Similarity search - Component
Biological speciesPROCHLORON DIDEMNI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsKoehnke, J. / Zollman, D. / Vendome, J. / Raab, A. / Houssen, W.E. / Smith, M.C. / Jaspars, M. / Naismith, J.H.
CitationJournal: Chembiochem / Year: 2012
Title: The Discovery of New Cyanobactins from Cyanothece Pcc 7425 Defines a New Signature for Processing of Patellamides.
Authors: Houssen, W.E. / Koehnke, J. / Zollman, D. / Vendome, J. / Raab, A. / Smith, M.C. / Naismith, J.H. / Jaspars, M.
History
DepositionAug 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Nov 6, 2013Group: Structure summary
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SUBTILISIN-LIKE PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,3731
Polymers29,3731
Non-polymers00
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.610, 130.610, 130.610
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 SUBTILISIN-LIKE PROTEIN


Mass: 29373.178 Da / Num. of mol.: 1 / Fragment: RESIDUES 10-289 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PROCHLORON DIDEMNI (bacteria) / Plasmid: PHISTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q52QI9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 218 TO ALA

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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: 2.99 Å3/Da / Density % sol: 58.92 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.58→92.36 Å / Num. obs: 48227 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.2
Reflection shellResolution: 1.58→1.62 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DBI

1dbi


Resolution: 1.58→92.36 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.077 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.17432 2580 5.1 %RANDOM
Rwork0.15552 ---
obs0.15643 48227 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.526 Å2
Refinement stepCycle: LAST / Resolution: 1.58→92.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 0 303 2308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192070
X-RAY DIFFRACTIONr_bond_other_d0.0010.021385
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9752823
X-RAY DIFFRACTIONr_angle_other_deg0.8893.0023382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2295281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13823.6984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67315321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8491517
X-RAY DIFFRACTIONr_chiral_restr0.0780.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02400
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.578→1.619 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 186 -
Rwork0.191 3411 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.476-2.91730.038219.8531-1.67690.1990.00960.19590.1772-0.26650.08530.4077-0.0038-0.0806-0.09490.1246-0.027-0.01470.1470.08010.0858-1245.36432.956
21.34390.3238-0.47012.7072-1.20562.1677-0.06320.12420.0009-0.26850.16560.20540.237-0.2229-0.10250.0609-0.0655-0.04260.09470.03840.0657-19.97734.51242.622
31.23860.26820.12511.3369-0.07672.8172-0.00830.0032-0.0962-0.09550.0523-0.05440.25720.1065-0.0440.04750.00040.0090.02080.00620.0251-2.01533.14247.992
41.58310.4888-0.48421.5348-0.82381.58340.0184-0.05490.1128-0.01220.03120.0442-0.05540.0255-0.04960.0306-0.01060.00180.01410.00470.018-4.4246.98443.549
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 21
2X-RAY DIFFRACTION2A22 - 96
3X-RAY DIFFRACTION3A97 - 196
4X-RAY DIFFRACTION4A197 - 289

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