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- PDB-3t8f: Thermolysin In Complex With UBTLN34 -

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Basic information

Entry
Database: PDB / ID: 3t8f
TitleThermolysin In Complex With UBTLN34
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-[(R)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-N-ETHYL-L-LEUCINAMIDE / Chem-UBU / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 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
DepositionAug 1, 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)35,73016
Polymers34,3601
Non-polymers1,37015
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.400, 92.400, 131.200
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-634-

HOH

21A-706-

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, 492 molecules

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


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 385.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H28N3O5P
References: N-[(R)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-N-ETHYL-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.: 5 / 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.: 477 / 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: 47.72 %
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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 14, 2010 / Details: Collimating Mirror
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. all: 60157 / Num. obs: 60157 / % possible obs: 99.7 % / Redundancy: 5 % / Rsym value: 0.062 / Net I/σ(I): 22
Reflection shellResolution: 1.44→1.46 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 5.4 / Num. unique all: 2836 / Rsym value: 0.272 / % possible all: 96.2

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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: 1.44→30.349 Å / SU ML: 0.15 / Cross valid method: FREE R / σ(F): 0 / Phase error: 13.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1586 2951 5.04 %RANDOM
Rwork0.1421 ---
all0.1429 61525 --
obs0.1429 58574 97.18 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.282 Å2 / ksol: 0.405 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2906 Å20 Å20 Å2
2---1.2906 Å2-0 Å2
3---2.5811 Å2
Refinement stepCycle: LAST / Resolution: 1.44→30.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 75 477 2984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122657
X-RAY DIFFRACTIONf_angle_d1.0483672
X-RAY DIFFRACTIONf_dihedral_angle_d15.128936
X-RAY DIFFRACTIONf_chiral_restr0.074384
X-RAY DIFFRACTIONf_plane_restr0.005468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.46360.17581310.16722488X-RAY DIFFRACTION93
1.4636-1.48880.21841230.17922493X-RAY DIFFRACTION93
1.4888-1.51590.20981380.16152508X-RAY DIFFRACTION94
1.5159-1.54510.14771360.1562551X-RAY DIFFRACTION95
1.5451-1.57660.14961480.14182529X-RAY DIFFRACTION95
1.5766-1.61090.19231260.14762565X-RAY DIFFRACTION96
1.6109-1.64840.15941140.1422639X-RAY DIFFRACTION97
1.6484-1.68960.16571340.13642609X-RAY DIFFRACTION97
1.6896-1.73530.13931440.13382606X-RAY DIFFRACTION97
1.7353-1.78630.17951490.13662613X-RAY DIFFRACTION97
1.7863-1.8440.19521280.13352633X-RAY DIFFRACTION97
1.844-1.90990.14781480.13542621X-RAY DIFFRACTION97
1.9099-1.98630.15611380.13682678X-RAY DIFFRACTION99
1.9863-2.07670.17771400.14252697X-RAY DIFFRACTION99
2.0767-2.18620.17061360.13782720X-RAY DIFFRACTION99
2.1862-2.32310.15191310.13382726X-RAY DIFFRACTION99
2.3231-2.50240.14941520.14242714X-RAY DIFFRACTION99
2.5024-2.7540.15731580.14042723X-RAY DIFFRACTION99
2.754-3.15220.14061420.14062775X-RAY DIFFRACTION100
3.1522-3.970.131780.13512793X-RAY DIFFRACTION100
3.97-30.35610.17551570.15172942X-RAY DIFFRACTION98
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)
10.1332-0.0634-0.03780.07670.05280.08690.01110.00390.00650.0669-0.0013-0.01480.0057-0.08020.00250.09710.00860.01560.11640.01130.064325.363828.52612.6584
20.10820.00740.03210.126-0.08080.06440.02050.0445-0.00820.0261-0.0313-0.0477-0.02270.02920.00510.06340.0019-0.00230.07380.00440.059131.122532.80464.1607
30.20710.03340.01510.1093-0.10040.10280.0217-0.0233-0.04380.0470.0048-0.0078-0.02080.008-0.01120.0640.00750.00440.06250.0030.051520.800926.1691.5896
40.12910.05290.05110.04620.00270.0338-0.0029-0.00160.0315-0.0131-0.01630.0219-0.01090.00220.00620.06120.00740.00890.0689-0.00080.057913.86136.2121-4.8248
50.04960.015-0.03350.19360.17670.27720.0584-0.10770.0410.0693-0.09040.04540.0415-0.03880.02810.0694-0.01140.0250.101-0.01470.08065.075531.77386.5066
60.13140.1420.07610.24050.0420.06250.0017-0.08630.0756-0.0106-0.05590.1381-0.0159-0.04040.0280.05320.0050.00330.0881-0.01210.113-4.803134.3983-7.3327
70.2210.01320.04610.2099-0.03580.1370.0547-0.0266-0.065-0.0328-0.00940.04350.02020.0322-0.02050.0797-0.0051-0.00050.0779-0.00710.08874.533918.1807-10.0917
80.11130.0410.05290.3170.00760.12530.03410.061-0.0494-0.0807-0.01360.11920.0497-0.0489-0.00080.0918-0.0072-0.01330.0948-0.01430.116-3.42120.7895-15.6894
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:19)
2X-RAY DIFFRACTION2(chain A and resid 20:60)
3X-RAY DIFFRACTION3(chain A and resid 61:100)
4X-RAY DIFFRACTION4(chain A and resid 101:173)
5X-RAY DIFFRACTION5(chain A and resid 174:202)
6X-RAY DIFFRACTION6(chain A and resid 203:256)
7X-RAY DIFFRACTION7(chain A and resid 257:274)
8X-RAY DIFFRACTION8(chain A and resid 275:316)

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