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- PDB-4n66: Thermolysin in complex with UBTLN37 -

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Basic information

Entry
Database: PDB / ID: 4n66
TitleThermolysin in complex with UBTLN37
ComponentsThermolysin
Keywordshydrolase/hydrolase inhibitor / Protease / Metalloprotease / Hydrolysis of peptide bonds / 2-Phosphoramidon / 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
N~2~-[(S)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-N-(2,2-DIMETHYLPROPYL)-L-LEUCINAMIDE / Chem-2GZ / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsKrimmer, S.G. / Heine, A. / Klebe, G.
CitationJournal: Chemmedchem / Year: 2014
Title: Methyl, Ethyl, Propyl, Butyl: Futile But Not for Water, as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors.
Authors: Krimmer, S.G. / Betz, M. / Heine, A. / Klebe, G.
History
DepositionOct 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Sep 20, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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.ptnr1_label_seq_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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

Deposited unit
E: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,60214
Polymers34,3601
Non-polymers1,24213
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.171, 92.171, 130.104
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11E-638-

HOH

21E-734-

HOH

31E-983-

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 / Fragment: Mature form (UNP residues 233-548) / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin

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Non-polymers , 6 types, 416 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 / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-2GZ / P-((((benzyloxy)carbonyl)amino)methyl)-N-((S)-4-methyl-1-(neopentylamino)-1-oxopentan-2-yl)phosphonamidic acid / N~2~-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-(2,2-dimethylpropyl)-L-leucinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 427.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H34N3O5P
References: N~2~-[(S)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-N-(2,2-DIMETHYLPROPYL)-L-LEUCINAMIDE
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

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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: 47.02 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM Tris/HCl, 1.9 M CsCl, 50% DMSO, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2012 / Details: Mirror
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. obs: 59295 / % possible obs: 99.6 % / Redundancy: 9 % / Biso Wilson estimate: 11.064 Å2 / Rsym value: 0.057 / Net I/σ(I): 39.2
Reflection shellResolution: 1.44→1.46 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 5 / Num. unique all: 2786 / Rsym value: 0.445 / % possible all: 96.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1492)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 8TLN

8tln


Resolution: 1.44→38.156 Å / SU ML: 0.1 / Cross valid method: R-free / σ(F): 1.34 / Phase error: 11.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1448 2988 5.04 %random
Rwork0.1121 ---
obs0.1137 59267 99.71 %-
all-59295 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→38.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2428 0 68 403 2899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052672
X-RAY DIFFRACTIONf_angle_d1.0683652
X-RAY DIFFRACTIONf_dihedral_angle_d13.115950
X-RAY DIFFRACTIONf_chiral_restr0.073380
X-RAY DIFFRACTIONf_plane_restr0.005484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4404-1.4640.19481470.14332517X-RAY DIFFRACTION96
1.464-1.48920.15871720.11852601X-RAY DIFFRACTION100
1.4892-1.51630.16021350.10872632X-RAY DIFFRACTION100
1.5163-1.54550.14821470.10472652X-RAY DIFFRACTION100
1.5455-1.5770.15931410.10222628X-RAY DIFFRACTION100
1.577-1.61130.15721500.10222649X-RAY DIFFRACTION100
1.6113-1.64880.14981160.09672682X-RAY DIFFRACTION100
1.6488-1.690.14531360.09692625X-RAY DIFFRACTION100
1.69-1.73570.13771560.09422668X-RAY DIFFRACTION100
1.7357-1.78680.12391300.092653X-RAY DIFFRACTION100
1.7868-1.84450.13131330.08862686X-RAY DIFFRACTION100
1.8445-1.91040.12511560.09932641X-RAY DIFFRACTION100
1.9104-1.98690.14061260.09792680X-RAY DIFFRACTION100
1.9869-2.07730.11981380.09962696X-RAY DIFFRACTION100
2.0773-2.18680.14241300.09972709X-RAY DIFFRACTION100
2.1868-2.32380.14521640.10242660X-RAY DIFFRACTION100
2.3238-2.50320.1381560.11392697X-RAY DIFFRACTION100
2.5032-2.7550.1491470.11522719X-RAY DIFFRACTION100
2.755-3.15350.1321450.122732X-RAY DIFFRACTION100
3.1535-3.97250.1451200.122811X-RAY DIFFRACTION100
3.9725-38.16960.16751430.14122941X-RAY DIFFRACTION99

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