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- PDB-4n4e: Thermolysin in complex with UBTLN58 -

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Basic information

Entry
Database: PDB / ID: 4n4e
TitleThermolysin in complex with UBTLN58
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-(3,3-DIMETHYLBUTYL)-L-LEUCINAMIDE / Chem-2G6 / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 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 8, 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)35,53813
Polymers34,3601
Non-polymers1,17812
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.505, 92.505, 131.488
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-540-

HOH

21E-961-

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, 474 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.: 3 / 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-2G6 / P-((((benzyloxy)carbonyl)amino)methyl)-N-((S)-1-((3,3-dimethylbutyl)amino)-4-methyl-1-oxopentan-2-yl)phosphonamidic acid / N~2~-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-(3,3-dimethylbutyl)-L-leucinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 441.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N3O5P
References: N~2~-[(S)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-N-(3,3-DIMETHYLBUTYL)-L-LEUCINAMIDE
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 47.95 %
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: Jul 19, 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: 1.13→50 Å / Num. obs: 118776 / % possible obs: 95.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 8.297 Å2 / Rsym value: 0.064 / Net I/σ(I): 32.6
Reflection shellResolution: 1.13→1.15 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 6.31 / Num. unique all: 4789 / Rsym value: 0.282 / % possible all: 78.7

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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: 1.13→31.814 Å / SU ML: 0.07 / Cross valid method: R-free / σ(F): 1.34 / Phase error: 11.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1375 5946 5.01 %random
Rwork0.1209 ---
obs0.1217 118650 95.91 %-
all-118733 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.13→31.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 65 462 2956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052673
X-RAY DIFFRACTIONf_angle_d1.1283652
X-RAY DIFFRACTIONf_dihedral_angle_d13.304953
X-RAY DIFFRACTIONf_chiral_restr0.08380
X-RAY DIFFRACTIONf_plane_restr0.005483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.14280.18541260.16353003X-RAY DIFFRACTION77
1.1428-1.15630.16071650.15763187X-RAY DIFFRACTION82
1.1563-1.17040.15762010.14893450X-RAY DIFFRACTION90
1.1704-1.18520.15022220.1383657X-RAY DIFFRACTION96
1.1852-1.20080.1322090.1233732X-RAY DIFFRACTION97
1.2008-1.21730.14221940.12493751X-RAY DIFFRACTION97
1.2173-1.23460.15241800.13283756X-RAY DIFFRACTION97
1.2346-1.25310.13382240.11733692X-RAY DIFFRACTION97
1.2531-1.27270.13971830.12013782X-RAY DIFFRACTION97
1.2727-1.29350.13332060.11723745X-RAY DIFFRACTION97
1.2935-1.31580.15081930.11733789X-RAY DIFFRACTION97
1.3158-1.33980.11851920.10573795X-RAY DIFFRACTION98
1.3398-1.36550.1421840.10043801X-RAY DIFFRACTION98
1.3655-1.39340.12292080.0953765X-RAY DIFFRACTION98
1.3934-1.42370.11031920.09763851X-RAY DIFFRACTION98
1.4237-1.45680.12011950.09743805X-RAY DIFFRACTION98
1.4568-1.49320.11341790.09833871X-RAY DIFFRACTION98
1.4932-1.53360.12172260.09933794X-RAY DIFFRACTION99
1.5336-1.57870.13191980.09993850X-RAY DIFFRACTION98
1.5787-1.62970.1352240.10053822X-RAY DIFFRACTION99
1.6297-1.68790.12081950.10253887X-RAY DIFFRACTION99
1.6879-1.75550.12881980.11043872X-RAY DIFFRACTION99
1.7555-1.83540.13342010.11383900X-RAY DIFFRACTION99
1.8354-1.93220.14062150.12273852X-RAY DIFFRACTION98
1.9322-2.05320.13532100.12033923X-RAY DIFFRACTION99
2.0532-2.21170.10871960.12043944X-RAY DIFFRACTION99
2.2117-2.43420.14642060.13043970X-RAY DIFFRACTION99
2.4342-2.78620.14032200.12873989X-RAY DIFFRACTION100
2.7862-3.50970.1512140.12873930X-RAY DIFFRACTION97
3.5097-31.82680.15211900.1413539X-RAY DIFFRACTION88

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