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- PDB-6sck: THERMOLYSIN IN COMPLEX WITH FRAGMENT J77 -

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Basic information

Entry
Database: PDB / ID: 6sck
TitleTHERMOLYSIN IN COMPLEX WITH FRAGMENT J77
ComponentsThermolysin
KeywordsHYDROLASE / THERMOLYSIN / METALLOPROTEASE / 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
D-ARGININE / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsMagari, F. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: THERMOLYSIN IN COMPLEX WITH FRAGMENT J77
Authors: Magari, F. / Heine, A. / Klebe, G.
History
DepositionJul 24, 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)35,35214
Polymers34,3601
Non-polymers99213
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-73 kcal/mol
Surface area12510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.790, 92.790, 129.452
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-703-

HOH

21E-714-

HOH

31E-773-

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 , 6 types, 308 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-DAR / D-ARGININE


Type: D-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 47.46 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50 MM TRIS/HCL, 1.9 M CSCL, 50% DMSO

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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 PILATUS 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: 1.41→50 Å / Num. obs: 63850 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 13.35 Å2 / CC1/2: 0.999 / Rsym value: 0.076 / Net I/σ(I): 20.1
Reflection shellResolution: 1.41→1.49 Å / Mean I/σ(I) obs: 4.5 / Num. unique obs: 10112 / CC1/2: 0.94 / Rsym value: 0.497 / % possible all: 99.8

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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: 1.41→46.39 Å / SU ML: 0.1064 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.6477
RfactorNum. reflection% reflection
Rfree0.1553 3193 5 %
Rwork0.1293 --
obs0.1306 63843 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.55 Å2
Refinement stepCycle: LAST / Resolution: 1.41→46.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 49 295 2756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652594
X-RAY DIFFRACTIONf_angle_d0.91563539
X-RAY DIFFRACTIONf_chiral_restr0.077373
X-RAY DIFFRACTIONf_plane_restr0.0061469
X-RAY DIFFRACTIONf_dihedral_angle_d11.7178894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.430.20971340.1492548X-RAY DIFFRACTION99.19
1.43-1.450.17771370.1322598X-RAY DIFFRACTION100
1.45-1.480.16811360.11942588X-RAY DIFFRACTION100
1.48-1.50.15961370.11722597X-RAY DIFFRACTION100
1.5-1.530.14671360.11252595X-RAY DIFFRACTION100
1.53-1.560.17061370.10992590X-RAY DIFFRACTION100
1.56-1.590.1671370.10772604X-RAY DIFFRACTION100
1.59-1.630.15731370.10992609X-RAY DIFFRACTION100
1.63-1.660.15111370.10572591X-RAY DIFFRACTION99.96
1.66-1.70.16971370.10712616X-RAY DIFFRACTION100
1.7-1.750.13741390.10352634X-RAY DIFFRACTION100
1.75-1.80.12191360.09942591X-RAY DIFFRACTION100
1.8-1.860.13411380.10532627X-RAY DIFFRACTION100
1.86-1.930.13731380.10982620X-RAY DIFFRACTION100
1.93-20.16361380.11322622X-RAY DIFFRACTION100
2-2.10.14751390.11422631X-RAY DIFFRACTION100
2.1-2.210.15181390.11482647X-RAY DIFFRACTION100
2.21-2.340.12611390.11172647X-RAY DIFFRACTION99.96
2.34-2.520.15661410.12072666X-RAY DIFFRACTION100
2.52-2.780.13881410.13072674X-RAY DIFFRACTION100
2.78-3.180.14161420.13882705X-RAY DIFFRACTION100
3.18-4.010.17031440.1452741X-RAY DIFFRACTION100
4.01-46.390.17641540.17042909X-RAY DIFFRACTION99.74

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