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- PDB-1os0: Thermolysin with an alpha-amino phosphinic inhibitor -

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Basic information

Entry
Database: PDB / ID: 1os0
TitleThermolysin with an alpha-amino phosphinic inhibitor
ComponentsThermolysin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / THERMOLYSIN / ALPHA-AMINO PHOSPHINIC COMPOUND / NEPRYLISIN / HYDROLASE / Metal-binding / Metalloprotease / Protease / Secreted / Zymogen / HYDROLASE-HYDROLASE INHIBITOR complex
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 / Thermolysin metallopeptidase, alpha-helical 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-0PQ / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSelkti, M. / Tomas, A. / Prange, T.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Interactions of a new alpha-aminophosphinic derivative inside the active site of TLN (thermolysin): a model for zinc-metalloendopeptidase inhibition.
Authors: Selkti, M. / Tomas, A. / Gaucher, J.F. / Prange, T. / Fournie-Zaluski, M.C. / Chen, H. / Roques, B.P.
#1: Journal: Biochemistry / Year: 1999
Title: Crystal structures of alpha-mercaptoacyldipeptides in the Thermolysin active site: Structural parameters for a Zn Monodentation or bidentation in metalloendopeptidases
Authors: Gaucher, J.F. / Selkti, M. / Tiraboschi, G. / Prange, T. / Roques, B.P. / Tomas, A. / Fournie-Zaluski, M.C.
History
DepositionMar 18, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionMar 25, 2003ID: 1no0
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1618
Polymers34,3621
Non-polymers7987
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Thermolysin
hetero molecules

A: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,32116
Polymers68,7252
Non-polymers1,59714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area5080 Å2
ΔGint-205 kcal/mol
Surface area23160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.782, 93.782, 132.249
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thermolysin / Thermostable neutral proteinase


Mass: 34362.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin

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Non-polymers , 5 types, 193 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-0PQ / N-{(2R)-3-[(S)-[(1R)-1-amino-2-phenylethyl](hydroxy)phosphoryl]-2-benzylpropanoyl}-L-phenylalanine


Type: peptide-like / Mass: 494.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H31N2O5P
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE CONFLICT IN UNP ENTRY P00800

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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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8
Details: DMSO, CaCl2, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1120 mg/mlprotein1drop
220 mMinhibitor1drop
350 mMTris acetate1reservoirpH8.0
40.5 Mcalcium acetate1reservoir
54 mMdithiothreitol1reservoir
61 mMsodium azide1reservoir
745 %(v/v)DMSO1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.972 / Wavelength: 0.968 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 11, 2002 / Details: CURVATED MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9721
20.9681
ReflectionResolution: 2.1→22.5 Å / Num. all: 23742 / Num. obs: 20940 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 5.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 4.1 / % possible all: 70.1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 19.9 Å / Num. obs: 23742 / % possible obs: 91.6 % / Redundancy: 5.2 %
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / % possible obs: 85.5 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 7.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA- TRUNCATEdata scaling
AMoREphasing
SHELXL-97refinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LNF

1lnf


Resolution: 2.1→10 Å / Num. parameters: 10652 / Num. restraintsaints: 10250 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2123 10 %RANDOM
Rwork0.147 ---
all-21413 --
obs-19094 100 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 2294.3 / Occupancy sum non hydrogen: 2659.15
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 44 186 2662
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.27
X-RAY DIFFRACTIONs_zero_chiral_vol0.028
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.049
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.103
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 19 Å / Num. reflection Rfree: 1903 / % reflection Rfree: 6 % / Rfactor Rfree: 0.173 / Rfactor Rwork: 0.146
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.27

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