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- PDB-6scu: THERMOLYSIN IN COMPLEX WITH FRAGMENT J88 -

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Basic information

Entry
Database: PDB / ID: 6scu
TitleTHERMOLYSIN IN COMPLEX WITH FRAGMENT J88
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
4-diazanyl-4-oxidanylidene-butanoic acid / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsMagari, F. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: THERMOLYSIN IN COMPLEX WITH FRAGMENT J88
Authors: Magari, F. / Heine, A. / Klebe, G.
History
DepositionJul 25, 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)34,7968
Polymers34,3601
Non-polymers4367
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-46 kcal/mol
Surface area12490 Å2
Unit cell
Length a, b, c (Å)92.307, 92.307, 129.622
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-704-

HOH

21E-713-

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, 260 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.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-88B / 4-diazanyl-4-oxidanylidene-butanoic acid


Mass: 132.118 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8N2O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.32 Å3/Da / Density % sol: 46.98 %
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: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. obs: 61953 / % possible obs: 100 % / Redundancy: 8.3 % / Biso Wilson estimate: 13.31 Å2 / CC1/2: 0.999 / Rsym value: 0.08 / Net I/σ(I): 18.9
Reflection shellResolution: 1.42→1.51 Å / Mean I/σ(I) obs: 4.4 / Num. unique obs: 9812 / CC1/2: 0.945 / Rsym value: 0.495 / % possible all: 99.9

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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: 1.42→46.15 Å / SU ML: 0.1013 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 13.3507
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.162 3097 5 %
Rwork0.1318 58849 -
obs0.1333 61946 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.41 Å2
Refinement stepCycle: LAST / Resolution: 1.42→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 18 253 2691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00652545
X-RAY DIFFRACTIONf_angle_d0.88163475
X-RAY DIFFRACTIONf_chiral_restr0.0756368
X-RAY DIFFRACTIONf_plane_restr0.0057462
X-RAY DIFFRACTIONf_dihedral_angle_d12.8586876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.22591370.15232604X-RAY DIFFRACTION99.56
1.44-1.470.18861380.13622631X-RAY DIFFRACTION100
1.47-1.490.19331390.12342627X-RAY DIFFRACTION100
1.49-1.520.16761370.11012618X-RAY DIFFRACTION100
1.52-1.550.1561390.10862638X-RAY DIFFRACTION100
1.55-1.580.1491380.10662625X-RAY DIFFRACTION100
1.58-1.610.15311390.1072631X-RAY DIFFRACTION100
1.61-1.650.16131400.11292661X-RAY DIFFRACTION100
1.65-1.690.15061380.11052627X-RAY DIFFRACTION100
1.69-1.740.16161400.11032657X-RAY DIFFRACTION100
1.74-1.790.15321390.10662648X-RAY DIFFRACTION100
1.79-1.850.1511410.10632661X-RAY DIFFRACTION100
1.85-1.910.14251390.11232644X-RAY DIFFRACTION100
1.91-1.990.13451400.10862666X-RAY DIFFRACTION100
1.99-2.080.14241400.11352669X-RAY DIFFRACTION99.96
2.08-2.190.13391420.11292687X-RAY DIFFRACTION99.96
2.19-2.330.14481410.11542679X-RAY DIFFRACTION100
2.33-2.510.14851420.12092700X-RAY DIFFRACTION100
2.51-2.760.16381430.13012716X-RAY DIFFRACTION100
2.76-3.160.16281440.13592731X-RAY DIFFRACTION100
3.16-3.980.17621460.14572780X-RAY DIFFRACTION100
3.98-46.150.18781550.18062949X-RAY DIFFRACTION99.74

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