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- PDB-1ssx: 0.83A resolution crystal structure of alpha-lytic protease at pH 8 -

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Basic information

Entry
Database: PDB / ID: 1ssx
Title0.83A resolution crystal structure of alpha-lytic protease at pH 8
ComponentsAlpha-lytic protease
KeywordsHYDROLASE / a-lytic protease / serine protease / protein folding / protein stability / packing distortion
Function / homology
Function and homology information


alpha-lytic endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Alpha-lytic protease prodomain / Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Alpha-lytic protease prodomain / Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / 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
Alpha-lytic protease
Similarity search - Component
Biological speciesLysobacter enzymogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / REFINEMENT OF 1TAL.PDB / Resolution: 0.83 Å
AuthorsFuhrmann, C.N. / Agard, D.A.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The 0.83A Resolution Crystal Structure of alpha-Lytic Protease Reveals the Detailed Structure of the Active Site and Identifies a Source of Conformational Strain.
Authors: Fuhrmann, C.N. / Kelch, B.A. / Ota, N. / Agard, D.A.
History
DepositionMar 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Alpha-lytic protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4447
Polymers19,8751
Non-polymers5686
Water8,413467
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.910, 65.910, 79.697
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-465-

HOH

21A-481-

HOH

31A-587-

HOH

41A-677-

HOH

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Components

#1: Protein Alpha-lytic protease / Alpha-lytic endopeptidase


Mass: 19875.131 Da / Num. of mol.: 1 / Fragment: Mature protease domain (residues 200-397)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Gene: ALPHA-LP / Plasmid: pALP12 / Production host: Escherichia coli (E. coli) / Strain (production host): D1210 / References: UniProt: P00778, alpha-lytic endopeptidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.3M lithium sulfate, 0.02M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.785 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 7, 2000
Details: flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.785 Å / Relative weight: 1
ReflectionResolution: 0.83→10 Å / Num. all: 187431 / Num. obs: 187431 / % possible obs: 99.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 28.5
Reflection shellResolution: 0.83→0.84 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3 / Num. unique all: 9176 / % possible all: 98.8

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: REFINEMENT OF 1TAL.PDB
Starting model: PDB ENTRY 1TAL

1tal


Resolution: 0.83→10 Å / Num. parameters: 19125 / Num. restraintsaints: 20884 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Hydrogen atoms were included in the refinement as "riding hydrogens", with position and geometry fixed to those values defined by SHELXL-97. Methyl and hydroxyl hydrogens on single-conformer ...Details: Hydrogen atoms were included in the refinement as "riding hydrogens", with position and geometry fixed to those values defined by SHELXL-97. Methyl and hydroxyl hydrogens on single-conformer sidechains were each positioned at a torsion angle that best satisfied positive difference electron density (using instructions HFIX 137 and HFIX 147, respectively). It should be noted that the length of donor-hydrogen bonds in this structure are likely shorter than their true internuclear distance; these bond lengths are defined by SHELXL-97 parameters. The positions of only four hydrogen atoms were allowed to refine freely: His57 HD1, His57 HE1, Ser214 HG, and Gly193 HN. During the final stages of refinement, geometrical restraints were released for all non-hydrogen atoms in residues with single conformations. See publication for more details.
RfactorNum. reflection% reflectionSelection details
Rfree0.0991 18758 10 %RANDOM
Rwork0.086 ---
all0.087 187385 --
obs0.087 187385 99.6 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 10.8 Å2
Refine analyzeNum. disordered residues: 23 / Occupancy sum hydrogen: 1362.61 / Occupancy sum non hydrogen: 1767.2
Refinement stepCycle: LAST / Resolution: 0.83→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1391 0 32 467 1890
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.025
X-RAY DIFFRACTIONs_angle_d0.046
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0181
X-RAY DIFFRACTIONs_zero_chiral_vol0.107
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.1
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.039
X-RAY DIFFRACTIONs_approx_iso_adps0.097

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