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- PDB-6sc0: THERMOLYSIN IN COMPLEX WITH FRAGMENT J22 -

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Basic information

Entry
Database: PDB / ID: 6sc0
TitleTHERMOLYSIN IN COMPLEX WITH FRAGMENT J22
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
BICARBONATE ION / ISOPROPYL ALCOHOL / Chem-L5Q / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsMagari, F. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: THERMOLYSIN IN COMPLEX WITH FRAGMENT J22
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

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Assembly

Deposited unit
E: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,11611
Polymers34,3601
Non-polymers75510
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-80 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.572, 92.572, 129.113
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-700-

HOH

21E-719-

HOH

31E-726-

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 , 8 types, 273 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.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#7: Chemical ChemComp-L5Q / 5-methyl-~{N}-[2,2,2-tris(fluoranyl)ethyl]-1,2-oxazole-3-carboxamide


Mass: 208.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7F3N2O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 47.07 %
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: 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: 1.53→50 Å / Num. obs: 49092 / % possible obs: 98.6 % / Redundancy: 5.4 % / Biso Wilson estimate: 16.29 Å2 / CC1/2: 0.999 / Rsym value: 0.05 / Net I/σ(I): 21.27
Reflection shellResolution: 1.53→1.62 Å / Mean I/σ(I) obs: 4.11 / Num. unique obs: 7698 / CC1/2: 0.923 / Rsym value: 0.464 / % possible all: 97.2

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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: 1.53→46.29 Å / SU ML: 0.1144 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.3267
RfactorNum. reflection% reflection
Rfree0.1664 2455 5 %
Rwork0.1454 --
obs0.1464 49089 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.43 Å2
Refinement stepCycle: LAST / Resolution: 1.53→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2413 0 39 263 2715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752573
X-RAY DIFFRACTIONf_angle_d0.94313519
X-RAY DIFFRACTIONf_chiral_restr0.0552372
X-RAY DIFFRACTIONf_plane_restr0.0064473
X-RAY DIFFRACTIONf_dihedral_angle_d11.39441466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.560.2051310.19162492X-RAY DIFFRACTION96.19
1.56-1.590.21351320.17682515X-RAY DIFFRACTION97.71
1.59-1.630.1971330.15942512X-RAY DIFFRACTION97.82
1.63-1.660.17351330.15822533X-RAY DIFFRACTION98.45
1.66-1.710.20041340.1512545X-RAY DIFFRACTION98.24
1.71-1.750.17241340.14672541X-RAY DIFFRACTION98.13
1.75-1.80.16561350.13882560X-RAY DIFFRACTION98.72
1.8-1.860.17751330.13522545X-RAY DIFFRACTION98.75
1.86-1.930.14221370.13362593X-RAY DIFFRACTION99.09
1.93-2.010.16741360.12882595X-RAY DIFFRACTION99.74
2.01-2.10.1451370.12482596X-RAY DIFFRACTION99.6
2.1-2.210.14451380.12812618X-RAY DIFFRACTION99.71
2.21-2.350.13241370.12282599X-RAY DIFFRACTION99.64
2.35-2.530.16661380.12612636X-RAY DIFFRACTION99.68
2.53-2.780.1331390.1332633X-RAY DIFFRACTION99.35
2.78-3.180.15311390.14392643X-RAY DIFFRACTION98.44
3.18-4.010.17761410.14632671X-RAY DIFFRACTION98.74
4.01-46.290.19411480.17812807X-RAY DIFFRACTION97.11
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.160761716709-0.03093781567370.1764196057440.0394490929521-0.01125501700730.1946284311810.042791487775-0.06841948531890.04214652420910.128782035720.0215057127171-0.0691147119248-0.0148373333171-0.03294527908153.19210613422E-50.1469436636530.0121418210320.009188631238860.1787920825060.0220074278260.12175271945628.026672456827.495396116811.0058239808
20.557585101861-0.0874926255080.3790247005740.3371701144580.00112951262620.3609601656430.018514394472-0.0177496561289-0.04823063493210.052401654461-0.0226923036438-0.0458875831923-0.02177972999580.006513989924947.09918997701E-60.1333801762860.01308568209170.01762068823660.1469707303690.01182426336560.1103403112725.968702766131.35651058024.60851792231
30.519888445678-0.02674236099560.1225946779350.120999706668-0.04949304964130.1081387531210.03243410037850.0612126497449-0.00405024357069-0.0414521136823-0.0519511472232-0.00880238590266-0.01055224310890.0004942058685576.70274309311E-60.1212759302430.02337044922260.01624774804670.1390107467090.007013830649620.1057657056220.728833817133.9414517709-4.53936234061
40.6055707456010.01785707638960.09681558443910.2649527077610.1957892645720.3460912690440.016265973279-0.03306119215970.000322601265106-0.013869711561-0.01887022700180.0392008417671-0.0211264142355-0.046019449119-5.93464513151E-60.1055995280080.01682452455590.02090067974340.1399981596090.007275107321850.129096471926.9449279927933.6412607602-1.2865028224
50.8456975170090.03646989205960.1788482348870.290130678729-0.03613410262870.7632743584680.024180031720.0557216522763-0.12514455619-0.0695053935525-0.04722230860080.132723563643-0.00429571223833-0.166426696054-0.000135743216090.1200624212520.00582290509690.01906299188790.16309757455-0.006260956758450.179026843333-1.7027797847227.1063961533-11.4840064131
60.0789346410456-0.1796748243720.02574335003320.4292890739690.1060193843481.799903473090.02344027988040.0795449671691-0.2235203621470.0970069350182-0.1305229562860.1026966245960.0123759569124-0.432301493578-0.02517056623190.117495613056-0.0615948170262-0.0054056152850.248041814135-0.05045670896230.310601790456-8.4711472931119.4349210646-13.0339101793
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'E' and (resid 26 through 88 )
3X-RAY DIFFRACTION3chain 'E' and (resid 89 through 122 )
4X-RAY DIFFRACTION4chain 'E' and (resid 123 through 211 )
5X-RAY DIFFRACTION5chain 'E' and (resid 212 through 296 )
6X-RAY DIFFRACTION6chain 'E' and (resid 297 through 316 )

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