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- PDB-3t8g: Thermolysin In Complex With UBTLN26 -

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Basic information

Entry
Database: PDB / ID: 3t8g
TitleThermolysin In Complex With UBTLN26
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 ...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]-L-LEUCYLGLYCINE / Chem-UBT / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)35,76016
Polymers34,3601
Non-polymers1,40015
Water7,963442
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, 130.800
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-550-

HOH

21A-552-

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, 457 molecules

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


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 415.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H26N3O7P
References: N-[(R)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-L-LEUCYLGLYCINE
#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.: 442 / 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: 47.9 %
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: 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: 1.5→50 Å / Num. all: 53702 / Num. obs: 53702 / % possible obs: 99.9 % / Redundancy: 20.7 % / Rsym value: 0.079 / Net I/σ(I): 41.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 18.5 % / Mean I/σ(I) obs: 6.6 / Num. unique all: 2620 / Rsym value: 0.499 / % possible all: 99.5

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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: 1.5→40.14 Å / SU ML: 0.16 / Cross valid method: FREE R / σ(F): 0 / Phase error: 13.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1562 2649 5.06 %RANDOM
Rwork0.1416 ---
all0.1423 54982 --
obs0.1423 52333 97.59 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.03 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.4543 Å2-0 Å20 Å2
2---1.4543 Å2-0 Å2
3---2.9086 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2428 0 77 442 2947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122657
X-RAY DIFFRACTIONf_angle_d1.0543672
X-RAY DIFFRACTIONf_dihedral_angle_d15.241932
X-RAY DIFFRACTIONf_chiral_restr0.075382
X-RAY DIFFRACTIONf_plane_restr0.005470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52730.2071210.17142444X-RAY DIFFRACTION93
1.5273-1.55670.18141310.16312468X-RAY DIFFRACTION94
1.5567-1.58850.17761460.15252468X-RAY DIFFRACTION95
1.5885-1.6230.16091330.14282507X-RAY DIFFRACTION95
1.623-1.66070.17661270.14082535X-RAY DIFFRACTION96
1.6607-1.70230.15431330.13952544X-RAY DIFFRACTION96
1.7023-1.74830.18261350.1392566X-RAY DIFFRACTION97
1.7483-1.79980.17641500.13542558X-RAY DIFFRACTION97
1.7998-1.85780.15261300.132570X-RAY DIFFRACTION97
1.8578-1.92420.16471500.13122592X-RAY DIFFRACTION98
1.9242-2.00130.1461310.13872640X-RAY DIFFRACTION99
2.0013-2.09240.18951370.14292648X-RAY DIFFRACTION99
2.0924-2.20270.16421470.1372673X-RAY DIFFRACTION100
2.2027-2.34070.14231410.1372657X-RAY DIFFRACTION99
2.3407-2.52140.14951500.14052668X-RAY DIFFRACTION99
2.5214-2.7750.16231480.14212698X-RAY DIFFRACTION100
2.775-3.17640.13281420.14022716X-RAY DIFFRACTION100
3.1764-4.00140.14941500.13442781X-RAY DIFFRACTION100
4.0014-40.15460.14261470.15312951X-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)
10.1736-0.12080.02050.14980.1920.64850.05330.17430.0831-0.02-0.0547-0.06370.01480.01570.00540.11050.00860.00150.14540.02830.117837.432324.02184.7586
20.36890.01150.18480.3274-0.04230.10240.0123-0.0255-0.0190.0442-0.0078-0.0155-0.0102-0.0027-0.00110.06890.00530.00750.0830.00260.053724.437531.89163.3552
30.21620.0701-0.13490.2213-0.07690.09120.05130.04650.03940.0068-0.01180.0888-0.057-0.0662-0.01410.09950.01010.02580.1219-0.03670.136610.546246.20137.6213
40.0688-0.00750.02610.06760.040.03710.0007-0.0075-0.0117-0.0125-0.01120.00990.009-0.00140.00340.06680.00810.00940.08760.00070.079.959330.5425-6.2914
50.11110.08160.14150.09150.12040.18890.0768-0.10890.08520.0773-0.10290.09850.0447-0.15650.03240.0944-0.01090.03480.1488-0.0280.11663.693635.597.6466
60.01940.0121-0.05160.17460.0320.162-0.0246-0.06380.0768-0.0163-0.01480.1999-0.0448-0.09810.00680.06150.00050.00420.1287-0.01690.1488-5.638536.74-5.6251
70.0743-0.0747-0.0370.1157-0.04820.21510.01570.0090.0202-0.13610.02010.10030.03470.0082-0.02740.14380.0065-0.03530.09250.00940.161.626446.0795-14.2781
80.19530.00980.1510.2205-0.03850.21540.03230.0018-0.0599-0.0357-0.02170.09320.0523-0.0739-0.00880.069-0.00290.00030.0962-0.01370.1077-0.791223.6149-11.2936
90.02510.0674-0.06060.38830.02280.3140.0680.116-0.2209-0.0439-0.02420.12730.0456-0.09860.01140.0923-0.0229-0.0230.1429-0.02960.1925-8.492119.7948-12.9823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:6)
2X-RAY DIFFRACTION2(chain A and resid 7:125)
3X-RAY DIFFRACTION3(chain A and resid 126:131)
4X-RAY DIFFRACTION4(chain A and resid 132:181)
5X-RAY DIFFRACTION5(chain A and resid 182:201)
6X-RAY DIFFRACTION6(chain A and resid 202:220)
7X-RAY DIFFRACTION7(chain A and resid 221:227)
8X-RAY DIFFRACTION8(chain A and resid 228:297)
9X-RAY DIFFRACTION9(chain A and resid 298:316)

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