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- PDB-4mxj: Thermolysin in complex with UBTLN35 -

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Basic information

Entry
Database: PDB / ID: 4mxj
TitleThermolysin in complex with UBTLN35
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 ...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~-[(R)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-N-PROPYL-L-LEUCINAMIDE / Chem-2G8 / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.349 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
DepositionSep 26, 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 / pdbx_struct_special_symmetry / 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_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)35,40412
Polymers34,3601
Non-polymers1,04411
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.567, 92.567, 130.779
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-523-

HOH

21E-945-

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, 475 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-2G8 / P-((((benzyloxy)carbonyl)amino)methyl)-N-((S)-4-methyl-1-oxo-1-(propylamino)pentan-2-yl)phosphonamidic acid / N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-propyl-L-leucinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 399.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H30N3O5P
References: N~2~-[(R)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-N-PROPYL-L-LEUCINAMIDE
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
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: Apr 26, 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: 1.35→50 Å / Num. obs: 70475 / % possible obs: 96.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 9.654 Å2 / Rsym value: 0.069 / Net I/σ(I): 17.9
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 3410 / Rsym value: 0.475 / % possible all: 95.1

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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: 8TLN

8tln


Resolution: 1.349→21.905 Å / SU ML: 0.1 / Cross valid method: R-free / σ(F): 1.35 / Phase error: 12.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1507 3540 5.03 %random
Rwork0.1162 ---
obs0.1179 70402 96.37 %-
all-70427 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.349→21.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 56 464 2950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052642
X-RAY DIFFRACTIONf_angle_d1.0773610
X-RAY DIFFRACTIONf_dihedral_angle_d13.36951
X-RAY DIFFRACTIONf_chiral_restr0.076379
X-RAY DIFFRACTIONf_plane_restr0.005476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.349-1.36750.19591330.14582579X-RAY DIFFRACTION94
1.3675-1.3870.17381290.13562591X-RAY DIFFRACTION95
1.387-1.40770.20381330.12882636X-RAY DIFFRACTION95
1.4077-1.42970.15811550.12232541X-RAY DIFFRACTION95
1.4297-1.45310.17161210.12012626X-RAY DIFFRACTION95
1.4531-1.47820.13631450.1122599X-RAY DIFFRACTION96
1.4782-1.50510.17551210.11192605X-RAY DIFFRACTION95
1.5051-1.5340.15371290.10832597X-RAY DIFFRACTION95
1.534-1.56530.15111520.10642585X-RAY DIFFRACTION94
1.5653-1.59930.15581500.10452580X-RAY DIFFRACTION95
1.5993-1.63650.15241380.09982600X-RAY DIFFRACTION95
1.6365-1.67740.1551410.10142611X-RAY DIFFRACTION95
1.6774-1.72280.16871380.09922625X-RAY DIFFRACTION95
1.7228-1.77340.13191360.10042641X-RAY DIFFRACTION96
1.7734-1.83070.15361510.09812626X-RAY DIFFRACTION96
1.8307-1.89610.13381640.09992665X-RAY DIFFRACTION97
1.8961-1.97190.13891410.10792712X-RAY DIFFRACTION97
1.9719-2.06160.12831530.10612713X-RAY DIFFRACTION98
2.0616-2.17020.14931560.10582745X-RAY DIFFRACTION99
2.1702-2.3060.14981350.11372774X-RAY DIFFRACTION99
2.306-2.48390.15391320.1222786X-RAY DIFFRACTION99
2.4839-2.73340.1561450.12662802X-RAY DIFFRACTION99
2.7334-3.1280.1341450.12182843X-RAY DIFFRACTION100
3.128-3.93720.1511690.11992861X-RAY DIFFRACTION100
3.9372-21.90750.15821280.13572919X-RAY DIFFRACTION95

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