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- PDB-4mzn: Thermolysin in complex with UBTLN59 -

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Basic information

Entry
Database: PDB / ID: 4mzn
TitleThermolysin in complex with UBTLN59
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~-[(S)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-N-[(2S)-2-METHYLBUTYL]-L-LEUCINAMIDE / Chem-2G9 / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.172 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 30, 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)35,51013
Polymers34,3601
Non-polymers1,15012
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.493, 92.493, 131.183
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-536-

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, 488 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.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-2G9 / P-((((benzyloxy)carbonyl)amino)methyl)-N-((S)-4-methyl-1-(((S)-2-methylbutyl)amino)-1-oxopentan- 2-yl)phosphonamidic acid / N~2~-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-[(2S)-2-methylbutyl]-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-[(2S)-2-METHYLBUTYL]-L-LEUCINAMIDE
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
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: 1.17→50 Å / Num. obs: 110592 / % possible obs: 99.3 % / Redundancy: 9.2 % / Biso Wilson estimate: 9.115 Å2 / Rsym value: 0.072 / Net I/σ(I): 29.1
Reflection shellResolution: 1.17→1.19 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.84 / Num. unique all: 4798 / Rsym value: 0.309 / % possible all: 87.9

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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: 1.172→20.706 Å / SU ML: 0.07 / Cross valid method: R-free / σ(F): 1.34 / Phase error: 11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1382 5530 5.01 %random
Rwork0.1158 ---
obs0.1169 110476 99.75 %-
all-110501 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.172→20.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 62 476 2967
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052670
X-RAY DIFFRACTIONf_angle_d1.1283647
X-RAY DIFFRACTIONf_dihedral_angle_d13.334947
X-RAY DIFFRACTIONf_chiral_restr0.08380
X-RAY DIFFRACTIONf_plane_restr0.005484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.172-1.18530.18361840.163291X-RAY DIFFRACTION96
1.1853-1.19920.1852100.13963414X-RAY DIFFRACTION99
1.1992-1.21390.16521630.14033458X-RAY DIFFRACTION100
1.2139-1.22920.1561850.1333439X-RAY DIFFRACTION100
1.2292-1.24540.14811660.1243478X-RAY DIFFRACTION100
1.2454-1.26250.13181620.11783497X-RAY DIFFRACTION100
1.2625-1.28050.13981870.11373444X-RAY DIFFRACTION100
1.2805-1.29960.14791790.11033455X-RAY DIFFRACTION100
1.2996-1.31990.13721800.10793471X-RAY DIFFRACTION100
1.3199-1.34150.1361580.10353498X-RAY DIFFRACTION100
1.3415-1.36470.10641790.09893467X-RAY DIFFRACTION100
1.3647-1.38950.13541820.09633474X-RAY DIFFRACTION100
1.3895-1.41620.1272080.09893441X-RAY DIFFRACTION100
1.4162-1.44510.10091800.09643500X-RAY DIFFRACTION100
1.4451-1.47650.1221960.09343447X-RAY DIFFRACTION100
1.4765-1.51080.11291760.09493502X-RAY DIFFRACTION100
1.5108-1.54860.12281700.09533484X-RAY DIFFRACTION100
1.5486-1.59050.10552040.0943472X-RAY DIFFRACTION100
1.5905-1.63730.12242030.09883488X-RAY DIFFRACTION100
1.6373-1.69010.12831660.10293513X-RAY DIFFRACTION100
1.6901-1.75040.14881640.1063522X-RAY DIFFRACTION100
1.7504-1.82050.13142200.10743484X-RAY DIFFRACTION100
1.8205-1.90330.13632100.11033480X-RAY DIFFRACTION100
1.9033-2.00360.13121840.11283533X-RAY DIFFRACTION100
2.0036-2.1290.12141880.11143530X-RAY DIFFRACTION100
2.129-2.29320.13391520.11563601X-RAY DIFFRACTION100
2.2932-2.52360.16541920.12213566X-RAY DIFFRACTION100
2.5236-2.88790.16041850.12453599X-RAY DIFFRACTION100
2.8879-3.63520.13091880.12133647X-RAY DIFFRACTION100
3.6352-20.70910.15052090.13653751X-RAY DIFFRACTION98

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