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- PDB-3t8c: Thermolysin In Complex With UBTLN30 -

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Basic information

Entry
Database: PDB / ID: 3t8c
TitleThermolysin In Complex With UBTLN30
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-LEUCYL-L-NORVALINE / Chem-UBW / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsBiela, A. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Thermolysin Inhibition
Authors: Biela, A. / Nasief, N. / Heine, A. / Hangauer, D. / 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 1.2Sep 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 / 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_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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)35,71015
Polymers34,3601
Non-polymers1,35014
Water7,782432
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, 130.400
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-393-

HOH

21A-750-

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, 446 molecules

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


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 457.458 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H32N3O7P
References: N-[(R)-({[(BENZYLOXY)CARBONYL]AMINO}METHYL)(HYDROXY)PHOSPHORYL]-L-LEUCYL-L-NORVALINE
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / 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.: 432 / 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: 47.63 %
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: 1.66→50 Å / Num. all: 39580 / Num. obs: 39580 / % possible obs: 99.7 % / Redundancy: 5.5 % / Rsym value: 0.054 / Net I/σ(I): 28.8
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 7.6 / Num. unique all: 1938 / Rsym value: 0.22 / % possible all: 99.7

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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: 1.66→43.631 Å / SU ML: 0.14 / Cross valid method: FREE R / σ(F): 0 / Phase error: 14.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1658 1949 5.04 %RANDOM
Rwork0.1391 ---
all0.1405 40654 --
obs0.1405 38705 97.64 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.239 Å2 / ksol: 0.381 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2182 Å20 Å20 Å2
2---2.2182 Å2-0 Å2
3---4.4365 Å2
Refinement stepCycle: LAST / Resolution: 1.66→43.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2428 0 74 432 2934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112641
X-RAY DIFFRACTIONf_angle_d1.033650
X-RAY DIFFRACTIONf_dihedral_angle_d13.124921
X-RAY DIFFRACTIONf_chiral_restr0.074382
X-RAY DIFFRACTIONf_plane_restr0.005467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6601-1.70160.21091550.16552467X-RAY DIFFRACTION94
1.7016-1.74760.19691280.15732519X-RAY DIFFRACTION95
1.7476-1.7990.17981140.14312550X-RAY DIFFRACTION96
1.799-1.85710.19191550.13272534X-RAY DIFFRACTION96
1.8571-1.92350.18741540.13322539X-RAY DIFFRACTION97
1.9235-2.00050.19031320.12992576X-RAY DIFFRACTION98
2.0005-2.09150.14731290.13042626X-RAY DIFFRACTION99
2.0915-2.20180.1611500.12432625X-RAY DIFFRACTION99
2.2018-2.33970.14121210.12892650X-RAY DIFFRACTION99
2.3397-2.52040.15681370.13332665X-RAY DIFFRACTION99
2.5204-2.7740.17541370.13672668X-RAY DIFFRACTION99
2.774-3.17530.14291330.13432712X-RAY DIFFRACTION99
3.1753-4.00010.15111550.13772751X-RAY DIFFRACTION100
4.0001-43.64640.17141490.1592874X-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)
10.2997-0.04480.14160.2552-0.09150.09010.0004-0.0374-0.01090.048-0.0003-0.0022-0.02060.00670.00430.04510.0080.01130.05940.00260.028924.790631.69083.4064
20.00570.01640.00760.16930.07010.02920.10330.09810.09090.00830.01770.0719-0.0608-0.0506-0.06570.06910.0220.0150.0963-0.0130.100510.94344.48077.5724
30.10180.06480.12170.21990.02380.1812-0.0018-0.04460.0255-0.0013-0.02450.095-0.0089-0.07250.00950.04210.00570.01280.0846-0.00750.07932.16832.8157-4.5653
40.381-0.1087-0.03790.2286-0.22610.77640.1157-0.0579-0.1427-0.0004-0.04850.05710.12150.0815-0.04430.0763-0.0048-0.00320.0736-0.01020.10015.570118.5029-10.9969
50.20820.175-0.1650.60110.22610.42650.03810.1237-0.1295-0.0649-0.04010.11620.0309-0.11590.0340.0655-0.0106-0.01430.1043-0.0270.1292-3.379120.8025-15.7815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:127)
2X-RAY DIFFRACTION2(chain A and resid 128:132)
3X-RAY DIFFRACTION3(chain A and resid 133:259)
4X-RAY DIFFRACTION4(chain A and resid 260:274)
5X-RAY DIFFRACTION5(chain A and resid 275:316)

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