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- PDB-4mwp: Thermolysin in complex with UBTLN46 -

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Basic information

Entry
Database: PDB / ID: 4mwp
TitleThermolysin in complex with UBTLN46
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-(2-PHENYLETHYL)-L-LEUCINAMIDE / Chem-2GC / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 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 25, 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_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)35,63614
Polymers34,3601
Non-polymers1,27613
Water7,800433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.518, 92.518, 130.977
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-874-

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, 446 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.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 461.491 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H32N3O5P
References: N~2~-[(R)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-N-(2-PHENYLETHYL)-L-LEUCINAMIDE
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 47.76 %
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 24, 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: 1.23→50 Å / Num. obs: 92439 / % possible obs: 96.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 8.807 Å2 / Rsym value: 0.068 / Net I/σ(I): 17.8
Reflection shellResolution: 1.23→1.25 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 3.92 / Num. unique all: 3704 / Rsym value: 0.207 / % possible all: 78.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8TLN

8tln


Resolution: 1.23→43.618 Å / SU ML: 0.07 / Cross valid method: R-free / σ(F): 1.34 / Phase error: 12.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1437 4634 5.02 %random
Rwork0.1181 ---
obs0.1194 92381 96.23 %-
all-92405 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.23→43.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2430 0 71 433 2934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062689
X-RAY DIFFRACTIONf_angle_d1.1183664
X-RAY DIFFRACTIONf_dihedral_angle_d14.63957
X-RAY DIFFRACTIONf_chiral_restr0.08378
X-RAY DIFFRACTIONf_plane_restr0.005486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2299-1.24390.19181030.16392276X-RAY DIFFRACTION76
1.2439-1.25860.20811300.15182464X-RAY DIFFRACTION82
1.2586-1.27390.19221310.14912550X-RAY DIFFRACTION85
1.2739-1.290.16291480.13312644X-RAY DIFFRACTION89
1.29-1.3070.15921450.12912689X-RAY DIFFRACTION90
1.307-1.32490.14761240.11872826X-RAY DIFFRACTION93
1.3249-1.34380.13561430.11672836X-RAY DIFFRACTION95
1.3438-1.36390.13681530.11572884X-RAY DIFFRACTION96
1.3639-1.38520.16431670.1112941X-RAY DIFFRACTION99
1.3852-1.40790.14061640.10833001X-RAY DIFFRACTION99
1.4079-1.43220.15791500.1062975X-RAY DIFFRACTION99
1.4322-1.45820.1381630.10262984X-RAY DIFFRACTION100
1.4582-1.48630.13441830.10042972X-RAY DIFFRACTION100
1.4863-1.51660.13511500.09913019X-RAY DIFFRACTION100
1.5166-1.54960.13151530.09773002X-RAY DIFFRACTION100
1.5496-1.58570.12811520.09543026X-RAY DIFFRACTION100
1.5857-1.62530.13211390.09833048X-RAY DIFFRACTION100
1.6253-1.66930.11321590.10163035X-RAY DIFFRACTION100
1.6693-1.71840.13051620.10452992X-RAY DIFFRACTION100
1.7184-1.77390.13181630.10713048X-RAY DIFFRACTION100
1.7739-1.83730.13461650.11053017X-RAY DIFFRACTION100
1.8373-1.91080.13081760.10933018X-RAY DIFFRACTION100
1.9108-1.99780.13131780.1143028X-RAY DIFFRACTION100
1.9978-2.10310.13821610.11023066X-RAY DIFFRACTION100
2.1031-2.23490.13941740.11323023X-RAY DIFFRACTION100
2.2349-2.40740.15171570.11823078X-RAY DIFFRACTION100
2.4074-2.64960.16971340.12633115X-RAY DIFFRACTION100
2.6496-3.0330.14191590.12453098X-RAY DIFFRACTION99
3.033-3.82090.14121840.12483094X-RAY DIFFRACTION98
3.8209-43.64590.15561640.14082998X-RAY DIFFRACTION89

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