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- PDB-6sc3: THERMOLYSIN IN COMPLEX WITH FRAGMENT J62 -

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Basic information

Entry
Database: PDB / ID: 6sc3
TitleTHERMOLYSIN IN COMPLEX WITH FRAGMENT J62
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
methyl L-phenylalaninate / BICARBONATE ION / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsMagari, F. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: THERMOLYSIN IN COMPLEX WITH FRAGMENT J62
Authors: Magari, F. / Heine, A. / Klebe, G.
History
DepositionJul 23, 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)34,9049
Polymers34,3601
Non-polymers5448
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-84 kcal/mol
Surface area12450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.760, 92.760, 129.004
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-658-

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, 197 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-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3
#5: Chemical ChemComp-0A9 / methyl L-phenylalaninate


Type: L-peptide linking / Mass: 179.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#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.: 189 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
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: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→46.38 Å / Num. obs: 29838 / % possible obs: 99.5 % / Redundancy: 8.9 % / Biso Wilson estimate: 18.88 Å2 / CC1/2: 0.998 / Rsym value: 0.08 / Net I/σ(I): 14.7
Reflection shellResolution: 1.82→1.93 Å / Mean I/σ(I) obs: 3.48 / Num. unique obs: 4713 / CC1/2: 0.908 / Rsym value: 0.471 / % possible all: 99.6

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Processing

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

Resolution: 1.82→46.38 Å / SU ML: 0.1333 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.2331
RfactorNum. reflection% reflection
Rfree0.2052 1491 5 %
Rwork0.1638 --
obs0.1659 29835 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.97 Å2
Refinement stepCycle: LAST / Resolution: 1.82→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 26 189 2626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832508
X-RAY DIFFRACTIONf_angle_d0.88853418
X-RAY DIFFRACTIONf_chiral_restr0.053363
X-RAY DIFFRACTIONf_plane_restr0.0065458
X-RAY DIFFRACTIONf_dihedral_angle_d9.60491426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.880.23451300.20452492X-RAY DIFFRACTION99.21
1.88-1.950.25081330.17792535X-RAY DIFFRACTION99.96
1.95-2.030.22941340.16722545X-RAY DIFFRACTION100
2.03-2.120.21831340.15442543X-RAY DIFFRACTION99.96
2.12-2.230.20561340.14922540X-RAY DIFFRACTION99.81
2.23-2.370.20211350.14852562X-RAY DIFFRACTION99.81
2.37-2.550.15521340.152554X-RAY DIFFRACTION99.56
2.55-2.810.20991360.15722585X-RAY DIFFRACTION99.82
2.81-3.210.19111370.16292599X-RAY DIFFRACTION99.67
3.21-4.050.2211380.16022622X-RAY DIFFRACTION98.96
4.05-46.380.19521460.17732767X-RAY DIFFRACTION98.21

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