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- PDB-4mtw: Thermolysin in complex with UBTLN36 -

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Basic information

Entry
Database: PDB / ID: 4mtw
TitleThermolysin in complex with UBTLN36
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-METHYLPROPYL)-L-LEUCINAMIDE / Chem-2G7 / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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 20, 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_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_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.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)35,49613
Polymers34,3601
Non-polymers1,13612
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.563, 92.563, 131.113
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-519-

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, 461 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-2G7 / P-((((benzyloxy)carbonyl)amino)methyl)-N-((S)-1-(isobutylamino)-4-methyl-1-oxopentan-2-yl)phosphonamidic acid / N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-(2-methylpropyl)-L-leucinamide


Type: Peptide-like / Class: Inhibitor / Mass: 413.448 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H32N3O5P
References: N~2~-[(R)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-N-(2-METHYLPROPYL)-L-LEUCINAMIDE
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 47.87 %
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: 1.32→50 Å / Num. obs: 76659 / % possible obs: 98 % / Redundancy: 4.1 % / Biso Wilson estimate: 9.953 Å2 / Rsym value: 0.065 / Net I/σ(I): 20.1
Reflection shellResolution: 1.32→1.34 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.25 / Num. unique all: 3237 / Rsym value: 0.421 / % possible all: 84.1

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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: PDB ENTRY 8TLN

8tln


Resolution: 1.32→31.776 Å / SU ML: 0.1 / Cross valid method: R-free / σ(F): 1.35 / Phase error: 13.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.154 3864 5.05 %random
Rwork0.1205 ---
obs0.1222 76584 97.92 %-
all-76600 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.32→31.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 61 449 2942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062639
X-RAY DIFFRACTIONf_angle_d1.0933608
X-RAY DIFFRACTIONf_dihedral_angle_d13.504955
X-RAY DIFFRACTIONf_chiral_restr0.077383
X-RAY DIFFRACTIONf_plane_restr0.005472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3193-1.33540.23571110.20172096X-RAY DIFFRACTION80
1.3354-1.35230.2387990.19022262X-RAY DIFFRACTION87
1.3523-1.37010.22071140.17222360X-RAY DIFFRACTION90
1.3701-1.38890.19531220.15692433X-RAY DIFFRACTION93
1.3889-1.40870.1981160.1582561X-RAY DIFFRACTION96
1.4087-1.42980.18931430.13962537X-RAY DIFFRACTION98
1.4298-1.45210.20931390.13352598X-RAY DIFFRACTION100
1.4521-1.47590.16511460.12212611X-RAY DIFFRACTION100
1.4759-1.50140.14991520.1132609X-RAY DIFFRACTION100
1.5014-1.52870.16041260.10782611X-RAY DIFFRACTION100
1.5287-1.55810.15011290.10082646X-RAY DIFFRACTION100
1.5581-1.58990.12811440.09972609X-RAY DIFFRACTION100
1.5899-1.62440.1191360.09742643X-RAY DIFFRACTION100
1.6244-1.66220.13451430.10032609X-RAY DIFFRACTION100
1.6622-1.70380.14791600.10252613X-RAY DIFFRACTION100
1.7038-1.74990.15051340.1022642X-RAY DIFFRACTION100
1.7499-1.80130.15871520.10162632X-RAY DIFFRACTION100
1.8013-1.85950.14111340.10582631X-RAY DIFFRACTION100
1.8595-1.92590.14471470.10662625X-RAY DIFFRACTION100
1.9259-2.0030.13711570.1072656X-RAY DIFFRACTION100
2.003-2.09420.12851210.10512669X-RAY DIFFRACTION100
2.0942-2.20460.14931420.11122672X-RAY DIFFRACTION100
2.2046-2.34260.13111530.11472643X-RAY DIFFRACTION100
2.3426-2.52340.15991470.12122689X-RAY DIFFRACTION100
2.5234-2.77730.14491340.12782697X-RAY DIFFRACTION100
2.7773-3.17880.16731660.12542703X-RAY DIFFRACTION100
3.1788-4.00370.15251540.12282754X-RAY DIFFRACTION100
4.0037-31.78490.15551430.1362909X-RAY DIFFRACTION99

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