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- PDB-3t74: Thermolysin In Complex With UBTLN27 -

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Basic information

Entry
Database: PDB / ID: 3t74
TitleThermolysin In Complex With UBTLN27
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]-L-LEUCYL-L-ALANINE / Chem-UBY / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 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)35,69615
Polymers34,3601
Non-polymers1,33614
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.600, 92.600, 131.000
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-572-

HOH

21A-573-

HOH

31A-601-

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, 513 molecules

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


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 429.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H28N3O7P
References: N-[(S)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-L-LEUCYL-L-ALANINE
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / 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 / Water


Mass: 18.015 Da / Num. of mol.: 499 / 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 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: Jun 25, 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: 1.28→50 Å / Num. all: 83375 / Num. obs: 83375 / % possible obs: 97.3 % / Redundancy: 5.7 % / Rsym value: 0.052 / Net I/σ(I): 30.4
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 5.3 / Num. unique all: 4026 / Rsym value: 0.326 / % possible all: 95.4

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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: 1.28→22.797 Å / SU ML: 0.1 / Cross valid method: FREE R / σ(F): 0 / Phase error: 9.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1271 4095 5.06 %RANDOM
Rwork0.1055 ---
all0.1065 85060 --
obs0.1065 80965 94.71 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.669 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.4496 Å2-0 Å20 Å2
2---2.4496 Å2-0 Å2
3---4.8992 Å2
Refinement stepCycle: LAST / Resolution: 1.28→22.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 74 499 3005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132690
X-RAY DIFFRACTIONf_angle_d1.3183727
X-RAY DIFFRACTIONf_dihedral_angle_d15.328957
X-RAY DIFFRACTIONf_chiral_restr0.084396
X-RAY DIFFRACTIONf_plane_restr0.007475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.29510.1751450.14022427X-RAY DIFFRACTION89
1.2951-1.31080.17681280.13382436X-RAY DIFFRACTION88
1.3108-1.32740.14691430.12072480X-RAY DIFFRACTION91
1.3274-1.34490.131320.11442490X-RAY DIFFRACTION90
1.3449-1.36330.12671470.10692487X-RAY DIFFRACTION90
1.3633-1.38280.12431280.09452533X-RAY DIFFRACTION91
1.3828-1.40340.12391270.10162521X-RAY DIFFRACTION92
1.4034-1.42540.14051170.09442532X-RAY DIFFRACTION91
1.4254-1.44870.13641230.08982566X-RAY DIFFRACTION92
1.4487-1.47370.10141410.08782550X-RAY DIFFRACTION93
1.4737-1.50050.1281470.0842600X-RAY DIFFRACTION94
1.5005-1.52940.12321390.08532567X-RAY DIFFRACTION94
1.5294-1.56060.12051300.07852655X-RAY DIFFRACTION94
1.5606-1.59450.11281350.07752604X-RAY DIFFRACTION95
1.5945-1.63160.10421440.07852638X-RAY DIFFRACTION95
1.6316-1.67240.11671060.08262683X-RAY DIFFRACTION96
1.6724-1.71760.11831250.08652703X-RAY DIFFRACTION96
1.7176-1.76810.10991510.0852659X-RAY DIFFRACTION96
1.7681-1.82510.11811470.08222666X-RAY DIFFRACTION97
1.8251-1.89030.09641460.08632730X-RAY DIFFRACTION96
1.8903-1.9660.11271500.08962699X-RAY DIFFRACTION97
1.966-2.05540.11461490.09522745X-RAY DIFFRACTION98
2.0554-2.16370.10671640.09152746X-RAY DIFFRACTION98
2.1637-2.29910.11641720.09742739X-RAY DIFFRACTION98
2.2991-2.47640.13331580.10882761X-RAY DIFFRACTION98
2.4764-2.72530.15431450.11522842X-RAY DIFFRACTION99
2.7253-3.11880.12841460.11432835X-RAY DIFFRACTION99
3.1188-3.92610.13941460.12182918X-RAY DIFFRACTION100
3.9261-22.80040.14471640.14693058X-RAY DIFFRACTION99

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