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- PDB-3t73: Thermolysin In Complex With UBTLN22 -

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Basic information

Entry
Database: PDB / ID: 3t73
TitleThermolysin In Complex With UBTLN22
ComponentsThermolysin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protease / metalloprotease / hydrolysis of peptide bonds / 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 / Thermolysin metallopeptidase, alpha-helical 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-[(S)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-N-METHYL-L-LEUCINAMIDE / Chem-UBX / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBiela, A. / Heine, A. / Klebe, G.
CitationJournal: Chemmedchem / Year: 2012
Title: Water makes the difference: rearrangement of water solvation layer triggers non-additivity of functional group contributions in protein-ligand binding.
Authors: Biela, A. / Betz, M. / Heine, A. / Klebe, G.
History
DepositionJul 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Sep 13, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,63815
Polymers34,3601
Non-polymers1,27814
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.700, 92.700, 130.100
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
11A-636-

HOH

21A-897-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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, 414 molecules

#2: Chemical ChemComp-UBX / N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-methyl-L-leucinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 371.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H26N3O5P
References: N-[(S)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-N-METHYL-L-LEUCINAMIDE
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 47.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 50 mM Tris, 1.9 M cesium chloride, 50% DMSO, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 14, 2009 / Details: Collimating mirror
RadiationMonochromator: Bartels / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 44226 / Num. obs: 44226 / % possible obs: 100 % / Redundancy: 16.3 % / Rsym value: 0.08 / Net I/σ(I): 35.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 15.1 % / Mean I/σ(I) obs: 6.5 / Num. unique all: 2164 / Rsym value: 0.495 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8TLN

8tln


Resolution: 1.6→43.662 Å / SU ML: 0.13 / Cross valid method: FREE R / σ(F): 0 / Phase error: 14.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1657 2135 5 %RANDOM
Rwork0.1428 ---
all0.1439 44799 --
obs0.1439 42664 96.65 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.59 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8873 Å20 Å20 Å2
2---1.8873 Å2-0 Å2
3---3.7746 Å2
Refinement stepCycle: LAST / Resolution: 1.6→43.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2428 0 70 400 2898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122657
X-RAY DIFFRACTIONf_angle_d1.0553675
X-RAY DIFFRACTIONf_dihedral_angle_d14.803934
X-RAY DIFFRACTIONf_chiral_restr0.075383
X-RAY DIFFRACTIONf_plane_restr0.005470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.63730.19061290.17312469X-RAY DIFFRACTION90
1.6373-1.67820.20941360.16412525X-RAY DIFFRACTION92
1.6782-1.72360.18381370.16192558X-RAY DIFFRACTION93
1.7236-1.77430.20571360.14642599X-RAY DIFFRACTION95
1.7743-1.83160.18421340.13912648X-RAY DIFFRACTION96
1.8316-1.8970.17071350.132608X-RAY DIFFRACTION95
1.897-1.9730.17421180.13042697X-RAY DIFFRACTION96
1.973-2.06280.15511410.13462709X-RAY DIFFRACTION98
2.0628-2.17150.15971670.13292708X-RAY DIFFRACTION99
2.1715-2.30760.17361460.13832743X-RAY DIFFRACTION99
2.3076-2.48570.16511420.13712747X-RAY DIFFRACTION98
2.4857-2.73590.1561540.14072771X-RAY DIFFRACTION98
2.7359-3.13160.16741470.14222820X-RAY DIFFRACTION99
3.1316-3.94510.14591510.13972869X-RAY DIFFRACTION100
3.9451-43.67810.16481620.15333058X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4191-0.0237-0.1630.29440.01990.1960.00930.0243-0.0004-0.0288-0.0140.01290.00580.00260.00150.0686-0.0111-0.0170.09110.0050.067420.7026-32.0052-0.8949
20.15930.0666-0.02280.13890.10810.1365-0.07050.05280.0188-0.0559-0.10270.0384-0.11-0.01760.10050.15170.0047-0.03570.21510.01180.12347.9545-23.0245-8.3647
30.0478-0.0589-0.060.12290.04390.2580.01440.108-0.11370.0215-0.04610.12470.0348-0.18080.02370.0961-0.003-0.02250.1573-0.02720.1573-1.6835-36.8950.0217
40.07570.0925-0.0220.1145-0.03290.03190.0282-0.0077-0.03850.117-0.00370.0658-0.00430.0127-0.00540.179-0.01920.04950.13040.01630.21091.5928-46.124514.3196
50.09780.0219-0.08770.0680.00620.0880.02390.03040.0422-0.0087-0.05640.0334-0.012-0.11420.00970.07840.0043-0.01030.1416-0.01510.1538-4.7821-26.67425.8278
60.52890.04890.01710.1423-0.17390.33220.04040.04370.14910.0657-0.02670.0261-0.09920.027-0.00590.1014-0.00370.00060.1071-0.01890.12827.0731-18.966914.3331
70.3401-0.1292-0.00710.74650.07170.17840.0231-0.16840.20880.1193-0.04690.1358-0.0854-0.11850.02460.11380.0110.01290.1418-0.0440.1843-2.3062-19.75615.9264
80.0785-0.05680.0380.0412-0.02750.01840.0311-0.13340.0087-0.0061-0.02320.0387-0.0411-0.02290.00230.11990.0212-0.00240.2269-0.02940.1839-10.3277-27.860215.0665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:178)
2X-RAY DIFFRACTION2(chain A and resid 179:184)
3X-RAY DIFFRACTION3(chain A and resid 185:220)
4X-RAY DIFFRACTION4(chain A and resid 221:227)
5X-RAY DIFFRACTION5(chain A and resid 228:264)
6X-RAY DIFFRACTION6(chain A and resid 265:274)
7X-RAY DIFFRACTION7(chain A and resid 275:310)
8X-RAY DIFFRACTION8(chain A and resid 311:316)

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