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- PDB-6sbk: THERMOLYSIN IN COMPLEX WITH FRAGMENT J13 -

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Basic information

Entry
Database: PDB / ID: 6sbk
TitleTHERMOLYSIN IN COMPLEX WITH FRAGMENT J13
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
1-(1,3-dimethyl-1H-pyrazol-5-yl)methanamine / ISOPROPYL ALCOHOL / (2,5-dimethylpyrazol-3-yl)methylcarbamic acid / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsMagari, F. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: THERMOLYSIN IN COMPLEX WITH FRAGMENT J13
Authors: Magari, F. / Heine, A. / Klebe, G.
History
DepositionJul 21, 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)35,29713
Polymers34,3601
Non-polymers93712
Water4,864270
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-42 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.561, 92.561, 129.273
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-708-

HOH

21E-728-

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, 282 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.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: 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
#6: Chemical ChemComp-47J / 1-(1,3-dimethyl-1H-pyrazol-5-yl)methanamine


Mass: 125.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11N3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-L4Z / (2,5-dimethylpyrazol-3-yl)methylcarbamic acid


Mass: 169.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11N3O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 47.13 %
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 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→46.28 Å / Num. obs: 54619 / % possible obs: 99.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 13.81 Å2 / CC1/2: 0.999 / Rsym value: 0.062 / Net I/σ(I): 20.24
Reflection shellResolution: 1.48→1.57 Å / Mean I/σ(I) obs: 3.99 / Num. unique obs: 8612 / CC1/2: 0.911 / Rsym value: 0.478 / % possible all: 98.3

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Processing

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

Resolution: 1.48→46.28 Å / SU ML: 0.1172 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.6511
RfactorNum. reflection% reflection
Rfree0.1692 2731 5 %
Rwork0.1504 --
obs0.1514 54619 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.41 Å2
Refinement stepCycle: LAST / Resolution: 1.48→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 0 50 270 2734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042581
X-RAY DIFFRACTIONf_angle_d0.75033523
X-RAY DIFFRACTIONf_chiral_restr0.0692369
X-RAY DIFFRACTIONf_plane_restr0.0043481
X-RAY DIFFRACTIONf_dihedral_angle_d16.0583895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.510.24171330.20332526X-RAY DIFFRACTION98.01
1.51-1.530.21181310.17942507X-RAY DIFFRACTION98.4
1.53-1.560.18541340.16772542X-RAY DIFFRACTION98.45
1.56-1.590.18761330.15952523X-RAY DIFFRACTION98.55
1.59-1.630.18151340.15222544X-RAY DIFFRACTION98.78
1.63-1.670.18781340.14752539X-RAY DIFFRACTION98.82
1.67-1.710.15541340.14972556X-RAY DIFFRACTION98.93
1.71-1.750.14171340.14562538X-RAY DIFFRACTION99.04
1.75-1.810.1641350.13752577X-RAY DIFFRACTION99.12
1.81-1.860.16331350.14582566X-RAY DIFFRACTION99.37
1.86-1.930.15711360.14382577X-RAY DIFFRACTION99.23
1.93-2.010.19521360.1412582X-RAY DIFFRACTION99.6
2.01-2.10.16761360.13812589X-RAY DIFFRACTION99.56
2.1-2.210.14981370.13732602X-RAY DIFFRACTION99.56
2.21-2.350.15381370.12772599X-RAY DIFFRACTION99.89
2.35-2.530.13071380.13412624X-RAY DIFFRACTION99.89
2.53-2.790.15941400.14042653X-RAY DIFFRACTION99.93
2.79-3.190.17411400.14732670X-RAY DIFFRACTION99.89
3.19-4.020.16711420.1522699X-RAY DIFFRACTION99.86
4.02-46.280.19051520.17862875X-RAY DIFFRACTION99.84
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)
10.3324303001420.09597620237040.04365942255340.147388477373-0.04686076326870.1485322527870.0812152768240.0577991670993-0.09106885137120.0287086518277-0.0262504621534-0.0409058810806-0.0265466914518-0.003071919126550.1893083881090.02227789074880.02274536365040.01948569541380.05181643972550.00594745963378-0.003253158348524.893755731331.35193322752.98445943925
20.01788666683890.01092410966930.009181663722980.009544890445170.001488173861170.004475617392250.0100494473140.04106122157260.0418680187658-0.03184762527330.026023804038-0.0196856087493-0.0183988973615-0.007183241410020.007378810519060.09994375190240.01887731934770.01331972503560.134174909808-0.007443883226530.10461950747512.88419083235.1732332805-4.3540065661
30.001293105116-0.000663598078002-0.002418179958810.0130285511450.01278133097830.01133592662830.0224452265282-0.0209172275173-0.0320495835745-0.0288614886961-0.02609219742510.0496521855435-0.0116526593899-0.008648368570777.82817943383E-60.07348714556710.01444343702890.004955716086120.108857870860.01014747095820.08949148318936.1087959171128.9771141168-6.16730160012
40.0106238917558-0.00026758837273-0.007783982586280.00670584226710.005656265032760.005442728479040.0307279929886-0.04894969147470.02942440197420.0216464751026-0.04010287273560.00905259990698-0.0366726428505-0.0836000606215-0.001524957918090.1073612072180.01169460915750.02691540643320.183232475705-0.01624032588640.13668744751.495251887235.27974772635.35267517934
50.006546402752380.003497249259840.00884351171670.01316689852470.01209831917190.0162517890374-0.06088118532320.0001135161427270.0163752360561-0.0444172340408-0.01279414430450.0367260274771-0.111614270237-0.0814350922992-0.004869707284820.1382648809130.0439508174733-0.01997319412690.149288173114-0.00992905426920.162228852124-2.9905256956640.5201891605-12.0983917837
60.03543692859270.01223151819570.03442746792820.0456716339990.003925197078520.04067931625710.0685306309429-0.0211399109085-0.149943182846-0.0731284586518-0.04055573136030.09506845247760.0670879752686-0.1293103420470.004795958860730.107984377265-0.00256794966921-0.002178279593560.156858555579-0.005077384237960.165760782634-1.2906406131722.6135047423-11.1824002755
70.0111271417485-0.00205044559657-0.001555364392190.00271740130236-5.28757463962E-50.001859478407280.04543273618030.0120078000843-0.04656733428120.0088075473393-0.006038808554690.005155978980880.0158676666437-0.1222046943630.007958833206790.109497603312-0.0313228416178-0.02737226759350.176621718189-0.01775617091480.224014657615-8.5221968387119.4975115751-13.0452334956
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 1 through 122 )
2X-RAY DIFFRACTION2chain 'E' and (resid 123 through 158 )
3X-RAY DIFFRACTION3chain 'E' and (resid 159 through 180 )
4X-RAY DIFFRACTION4chain 'E' and (resid 181 through 211 )
5X-RAY DIFFRACTION5chain 'E' and (resid 212 through 232 )
6X-RAY DIFFRACTION6chain 'E' and (resid 233 through 296 )
7X-RAY DIFFRACTION7chain 'E' and (resid 297 through 316 )

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