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- PDB-6sb9: Thermolysin in complex with J28 -

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Basic information

Entry
Database: PDB / ID: 6sb9
TitleThermolysin in complex with J28
ComponentsThermolysin
KeywordsHYDROLASE / METALLOPROTEASE / HYDROLASE FRAGMENT COMPLEX
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
2-(pyridin-3-yl)ethanamine / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMagari, F. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Thermolysin in complex with J28
Authors: Magari, F. / Heine, A. / Klebe, G.
History
DepositionJul 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)35,09912
Polymers34,3601
Non-polymers73911
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-77 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.831, 92.831, 129.129
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-714-

HOH

21E-765-

HOH

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Components

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Protein , 1 types, 1 molecules E

#1: Protein Thermolysin / Thermostable neutral proteinase


Mass: 34360.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin

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Non-polymers , 5 types, 337 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-45X / 2-(pyridin-3-yl)ethanamine


Mass: 122.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10N2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 50 MM TRIS/HCL, 1.9 M CSCL, 50% DMSO, PH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.3→46.45 Å / Num. obs: 80826 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 12.14 Å2 / CC1/2: 0.999 / Rsym value: 0.058 / Net I/σ(I): 21.18
Reflection shellResolution: 1.3→1.38 Å / Mean I/σ(I) obs: 4.07 / Num. unique obs: 12774 / CC1/2: 0.92 / Rsym value: 0.49 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
MxCuBEdata collection
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.3→46.42 Å / SU ML: 0.0948 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.4342
RfactorNum. reflection% reflection
Rfree0.1514 4042 5 %
Rwork0.1268 --
obs0.1281 80820 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.83 Å2
Refinement stepCycle: LAST / Resolution: 1.3→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2410 0 34 326 2770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622591
X-RAY DIFFRACTIONf_angle_d0.91363538
X-RAY DIFFRACTIONf_chiral_restr0.0782373
X-RAY DIFFRACTIONf_plane_restr0.006477
X-RAY DIFFRACTIONf_dihedral_angle_d14.6931896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.23081360.17132587X-RAY DIFFRACTION98.59
1.31-1.330.17211350.14752563X-RAY DIFFRACTION99.41
1.33-1.350.19131390.13492627X-RAY DIFFRACTION99.57
1.35-1.370.17211370.1342603X-RAY DIFFRACTION99.64
1.37-1.380.1971360.12742587X-RAY DIFFRACTION99.67
1.38-1.40.16561370.12572602X-RAY DIFFRACTION99.49
1.4-1.430.16371370.11982599X-RAY DIFFRACTION99.78
1.43-1.450.13131380.11982623X-RAY DIFFRACTION99.75
1.45-1.470.15641360.11312601X-RAY DIFFRACTION99.71
1.47-1.50.16851380.1122619X-RAY DIFFRACTION99.89
1.5-1.520.14261370.10662603X-RAY DIFFRACTION99.78
1.52-1.550.1331380.10742619X-RAY DIFFRACTION99.93
1.55-1.580.14661390.10182635X-RAY DIFFRACTION99.89
1.58-1.620.13321370.10092615X-RAY DIFFRACTION99.96
1.62-1.660.13951400.1022652X-RAY DIFFRACTION99.96
1.66-1.70.12631380.10142616X-RAY DIFFRACTION100
1.7-1.740.1371390.10622643X-RAY DIFFRACTION100
1.74-1.80.12761390.10142635X-RAY DIFFRACTION100
1.8-1.850.16081390.10922649X-RAY DIFFRACTION100
1.85-1.920.14331390.10682643X-RAY DIFFRACTION100
1.92-20.13841400.11012654X-RAY DIFFRACTION100
2-2.090.12261400.11352662X-RAY DIFFRACTION99.93
2.09-2.20.12061400.11422665X-RAY DIFFRACTION100
2.2-2.330.14021410.11392676X-RAY DIFFRACTION99.96
2.33-2.520.14431420.12222699X-RAY DIFFRACTION100
2.52-2.770.14911410.12772676X-RAY DIFFRACTION99.61
2.77-3.170.16051440.13362732X-RAY DIFFRACTION100
3.17-3.990.14441450.14242766X-RAY DIFFRACTION99.97
3.99-46.420.18751550.16682927X-RAY DIFFRACTION99.39

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