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- PDB-9ozy: Gradient equilibration of hexagonal thermolysin to low salt over ... -

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Basic information

Entry
Database: PDB / ID: 9ozy
TitleGradient equilibration of hexagonal thermolysin to low salt over 15 minutes
ComponentsThermolysin
KeywordsHYDROLASE / Glycosidase
Function / homology
Function and homology information


thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif ...PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
LYSINE / VALINE / Thermolysin
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsJuers, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM090248 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Automated gradient equilibration of macromolecular crystals to new solution conditions.
Authors: Juers, D.H. / Quire, J. / Stothers, S.
History
DepositionJun 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9319
Polymers34,3621
Non-polymers5688
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.572, 93.572, 131.042
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11E-719-

HOH

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Components

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Protein , 1 types, 1 molecules E

#1: Protein Thermolysin / Neutral protease


Mass: 34362.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Geobacillus stearothermophilus (bacteria) / References: UniProt: P43133, thermolysin

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Non-polymers , 6 types, 250 molecules

#2: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: well: 2 M AmSO4; Drop: 45% DMSO

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Data collection

DiffractionMean temperature: 294 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: May 28, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→29.71 Å / Num. obs: 34729 / % possible obs: 99.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 19.5 Å2 / CC1/2: 0.982 / Net I/σ(I): 6.1
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 1851 / CC1/2: 0.341

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→29.71 Å / SU ML: 0.2049 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.8667
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.187 1787 5.16 %
Rwork0.1586 32861 -
obs0.16 34648 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.46 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 26 242 2700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00982516
X-RAY DIFFRACTIONf_angle_d1.07793423
X-RAY DIFFRACTIONf_chiral_restr0.062364
X-RAY DIFFRACTIONf_plane_restr0.009452
X-RAY DIFFRACTIONf_dihedral_angle_d13.8011870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.80.35181310.34112453X-RAY DIFFRACTION98.93
1.8-1.850.36511170.31072471X-RAY DIFFRACTION99.5
1.85-1.910.28071440.26352474X-RAY DIFFRACTION99.17
1.91-1.980.25441480.21882450X-RAY DIFFRACTION99.31
1.98-2.060.23131360.20052479X-RAY DIFFRACTION98.9
2.06-2.150.22261450.18342473X-RAY DIFFRACTION99.32
2.15-2.260.19081360.14972520X-RAY DIFFRACTION99.7
2.26-2.410.17671350.13932509X-RAY DIFFRACTION99.92
2.41-2.590.16391350.1422537X-RAY DIFFRACTION100
2.59-2.850.17121330.14052548X-RAY DIFFRACTION100
2.85-3.260.17911400.142565X-RAY DIFFRACTION99.96
3.27-4.110.151430.11872609X-RAY DIFFRACTION100
4.11-29.710.13871440.13042773X-RAY DIFFRACTION99.86

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