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- PDB-6yms: Structural and Kinetic Evaluation of Phosphoramidate Inhibitors o... -

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Basic information

Entry
Database: PDB / ID: 6yms
TitleStructural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin
ComponentsThermolysin
KeywordsHYDROLASE / Phosphoramidate Inhibitor / Protease
Function / homology
Function and homology information


thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain ...Elastase; domain 1 - #10 / Elastase; domain 1 / 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 / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-OZH / Thermolysin
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsKljajic, M. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Structural and Kinetic Evaluation of Phosphoramidate Inhibitors on Thermolysin
Authors: Kljajic, M. / Gerber, H.-D. / Heine, A. / Klebe, G.
History
DepositionApr 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)35,54012
Polymers34,3601
Non-polymers1,18011
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-41 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.619, 92.619, 129.982
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-779-

HOH

21E-806-

HOH

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Components

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Protein , 1 types, 1 molecules E

#1: Protein Thermolysin / Neutral protease


Mass: 34360.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: nprS, nprM / Production host: Geobacillus stearothermophilus (bacteria) / References: UniProt: P43133, thermolysin

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Non-polymers , 7 types, 373 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-OZH / (2~{S})-4-methyl-2-[2-[[oxidanyl-[(1~{S})-2-phenyl-1-(phenylmethoxycarbonylamino)ethyl]phosphoryl]amino]ethanoylamino]pentanoic acid


Mass: 505.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32N3O7P / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.0 M CsCl, 50 mM Tris(hydroxymethyl)aminomethane

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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 2M / Detector: PIXEL / Date: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.32→46.31 Å / Num. obs: 76712 / % possible obs: 98.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 16.91 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.083 / Rsym value: 0.08 / Net I/σ(I): 19.89
Reflection shellResolution: 1.32→1.4 Å / Mean I/σ(I) obs: 4.55 / Num. unique obs: 12067 / CC1/2: 0.94 / Rrim(I) all: 0.516 / Rsym value: 0.495

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LVD

5lvd


Resolution: 1.32→46.31 Å / SU ML: 0.0813 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.3655
RfactorNum. reflection% reflection
Rfree0.1479 3836 5 %
Rwork0.1156 --
obs0.1173 76711 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 13.55 Å2
Refinement stepCycle: LAST / Resolution: 1.32→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 66 362 2844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062654
X-RAY DIFFRACTIONf_angle_d0.94813626
X-RAY DIFFRACTIONf_chiral_restr0.0785382
X-RAY DIFFRACTIONf_plane_restr0.006501
X-RAY DIFFRACTIONf_dihedral_angle_d17.1489950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.340.1941370.12822612X-RAY DIFFRACTION97.41
1.34-1.350.16451380.11642618X-RAY DIFFRACTION97.77
1.35-1.370.15821380.11992624X-RAY DIFFRACTION97.77
1.37-1.390.16391380.11352623X-RAY DIFFRACTION98.19
1.39-1.410.15421400.10832643X-RAY DIFFRACTION98.06
1.41-1.440.14831380.10782641X-RAY DIFFRACTION98.44
1.44-1.460.15171400.10392653X-RAY DIFFRACTION98.41
1.46-1.480.14731390.10012644X-RAY DIFFRACTION98.44
1.48-1.510.15071400.09772653X-RAY DIFFRACTION98.55
1.51-1.540.12771410.09352683X-RAY DIFFRACTION98.78
1.54-1.570.11841400.09262661X-RAY DIFFRACTION98.87
1.57-1.610.14951400.09462659X-RAY DIFFRACTION98.73
1.61-1.640.13121410.09192667X-RAY DIFFRACTION99.05
1.64-1.680.12491410.09582683X-RAY DIFFRACTION98.91
1.68-1.730.14891390.09822650X-RAY DIFFRACTION98.69
1.73-1.780.14281430.09952716X-RAY DIFFRACTION99.2
1.78-1.840.13021420.09832688X-RAY DIFFRACTION99.4
1.84-1.90.12221420.10042706X-RAY DIFFRACTION99.55
1.9-1.980.13811430.09872716X-RAY DIFFRACTION99.44
1.98-2.070.11321430.10172719X-RAY DIFFRACTION99.65
2.07-2.180.13251430.09842724X-RAY DIFFRACTION99.69
2.18-2.320.12741460.10342768X-RAY DIFFRACTION99.93
2.32-2.490.12171430.10432722X-RAY DIFFRACTION98.9
2.49-2.750.1331460.11152768X-RAY DIFFRACTION99.97
2.75-3.140.1531470.12172801X-RAY DIFFRACTION100
3.14-3.960.17351500.13652841X-RAY DIFFRACTION100
3.96-46.310.19021580.1662992X-RAY DIFFRACTION99.03

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