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- PDB-6sc1: THERMOLYSIN IN COMPLEX WITH FRAGMENT J96 -

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Basic information

Entry
Database: PDB / ID: 6sc1
TitleTHERMOLYSIN IN COMPLEX WITH FRAGMENT J96
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
ISOPROPYL ALCOHOL / ~{N}-oxidanylbicyclo[2.2.1]heptane-1-carboxamide / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsMagari, F. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: THERMOLYSIN IN COMPLEX WITH FRAGMENT J96
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)35,40415
Polymers34,3601
Non-polymers1,04414
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-47 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.797, 92.797, 129.056
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

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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 , 7 types, 231 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-L5W / ~{N}-oxidanylbicyclo[2.2.1]heptane-1-carboxamide


Mass: 155.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 47.31 %
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 PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 47287 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 16.66 Å2 / CC1/2: 0.999 / Rsym value: 0.067 / Net I/σ(I): 23.95
Reflection shellResolution: 1.56→1.65 Å / Mean I/σ(I) obs: 4.83 / Num. unique obs: 7457 / CC1/2: 0.94 / Rsym value: 0.494 / % possible all: 99.4

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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: 1.56→50 Å / SU ML: 0.1262 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.5314
RfactorNum. reflection% reflection
Rfree0.1751 2365 5 %
Rwork0.1509 --
obs0.1521 47281 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.18 Å2
Refinement stepCycle: LAST / Resolution: 1.56→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 56 217 2693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082560
X-RAY DIFFRACTIONf_angle_d0.93013486
X-RAY DIFFRACTIONf_chiral_restr0.0568368
X-RAY DIFFRACTIONf_plane_restr0.0065456
X-RAY DIFFRACTIONf_dihedral_angle_d12.08711449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.590.20741340.17462537X-RAY DIFFRACTION98.38
1.59-1.630.20421360.1662598X-RAY DIFFRACTION100
1.63-1.660.2011370.16852593X-RAY DIFFRACTION100
1.66-1.710.22061370.16262599X-RAY DIFFRACTION100
1.71-1.750.21281370.15952613X-RAY DIFFRACTION100
1.75-1.80.19931360.14582587X-RAY DIFFRACTION100
1.8-1.860.18731380.14122617X-RAY DIFFRACTION100
1.86-1.930.17311380.14262621X-RAY DIFFRACTION100
1.93-20.17611370.14072604X-RAY DIFFRACTION100
2-2.10.15011390.13492635X-RAY DIFFRACTION100
2.1-2.210.18121390.1352634X-RAY DIFFRACTION100
2.21-2.340.15931380.13532633X-RAY DIFFRACTION100
2.34-2.530.16911400.1342656X-RAY DIFFRACTION99.96
2.53-2.780.16931400.14572670X-RAY DIFFRACTION100
2.78-3.180.15931420.15072695X-RAY DIFFRACTION100
3.18-4.010.1931440.15252724X-RAY DIFFRACTION100
4.01-46.40.1621530.17192900X-RAY DIFFRACTION99.71
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)
10.768076240025-0.002401980161860.2718431637760.6220354339270.05679503778440.4212802012060.0180131249053-0.00994210379176-0.007139504477970.0575887856883-0.0347836379498-0.05067385103110.00103488338669-0.0131229486456-0.007905619475150.09861261616220.0199308465930.0231063514290.1207075993730.006854147581010.080131397480422.320486095432.25583451441.39332663989
20.0579862316428-0.0370876745868-0.0614109028380.01781719816540.03150269435730.05528444897470.0383842765643-0.0259280380687-0.0399812314142-0.0273074103846-0.03372188271720.08330090292280.0190966983702-0.0263310727261-3.45782977422E-60.1139543942310.01425973178290.0333550256750.1732612982680.003574464973970.1677079719015.9367628398129.0772228351-6.44554206113
30.03494865796570.04267426358740.007796484729330.04820549176990.05270352591790.230570531564-0.00543271334456-0.2450719724130.02462004211210.0356240946971-0.04520896433520.109582516512-0.0338774427314-0.2097365880030.005353896935910.1301235584250.02082725345770.05586162285880.238483806449-0.03203353659240.1743688545561.4040612181435.37369464734.93850652686
40.4815095543270.005708904187210.1725224582420.312586689666-0.1874760495280.4594300187130.02372144629330.0812271664264-0.117089342088-0.093657770556-0.04193193559170.154076991442-0.00550702882872-0.249166746773-0.01338794696880.103708847625-0.004235257981830.03124225349810.178144567252-0.02507331139410.202190640852-1.8978101681727.2645002874-11.7127615822
50.0536241122262-0.126756407401-0.02573361953370.32789394608-0.071937693040.962961920289-0.004357162471110.159606600235-0.2156374790380.0613936238649-0.0504643650720.0992977219910.062955165784-0.342922123423-0.01417555238830.125741076452-0.07409445994380.0180660614560.251114944858-0.05829130652270.345806861285-8.5631811034719.4620396402-13.3695339912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 1 through 158 )
2X-RAY DIFFRACTION2chain 'E' and (resid 159 through 180 )
3X-RAY DIFFRACTION3chain 'E' and (resid 181 through 211 )
4X-RAY DIFFRACTION4chain 'E' and (resid 212 through 296 )
5X-RAY DIFFRACTION5chain 'E' and (resid 297 through 316 )

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