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- PDB-4d91: Thermolysin In Complex With DMSO And Acetate -

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Basic information

Entry
Database: PDB / ID: 4d91
TitleThermolysin In Complex With DMSO And Acetate
ComponentsThermolysin
KeywordsHYDROLASE / protease / metalloprotease / hydrolysis of peptide bonds / phosphoramidon
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
ACETATE ION / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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
DepositionJan 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)34,8019
Polymers34,3601
Non-polymers4418
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.425, 93.425, 129.923
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-767-

HOH

21A-777-

HOH

31A-830-

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 , 5 types, 376 molecules

#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.9 M cesium chloride, 50% DMSO, 50 mM Tris, 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: 1.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 25, 2010 / Details: Collimating Mirror
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 49334 / Num. obs: 49334 / % possible obs: 98.3 % / Redundancy: 30.6 % / Rsym value: 0.056 / Net I/σ(I): 82.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 27.5 % / Mean I/σ(I) obs: 11.3 / Num. unique all: 1247 / Rsym value: 0.333 / % possible all: 95.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→34.34 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1844 1292 4.9 %RANDOM
Rwork0.1498 ---
all0.1515 51241 --
obs0.1515 48848 97.74 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.182 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2031 Å2-0 Å20 Å2
2---1.2031 Å2-0 Å2
3---2.4063 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 17 368 2808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172537
X-RAY DIFFRACTIONf_angle_d0.9793511
X-RAY DIFFRACTIONf_dihedral_angle_d12.526859
X-RAY DIFFRACTIONf_chiral_restr0.072366
X-RAY DIFFRACTIONf_plane_restr0.004449
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.93890.26591370.2543258593
1.9389-1.9810.27661280.2139265394
1.981-2.02710.24081250.1773269395
2.0271-2.07780.24061480.1561266296
2.0778-2.1340.17841160.141270796
2.134-2.19670.21841340.1389269497
2.1967-2.26760.20461640.1375272098
2.2676-2.34870.19441600.1264271698
2.3487-2.44270.16751230.1316278198
2.4427-2.55380.20811390.138274398
2.5538-2.68840.21651430.1441277999
2.6884-2.85680.1761350.1471277699
2.8568-3.07720.1841490.1515278299
3.0772-3.38660.16531410.15562791100
3.3866-3.87610.13861460.14252793100
3.8761-4.88130.16741390.12772795100
4.8813-34.34550.16921660.17542785100
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)
10.67420.21720.49980.87310.11230.3730.09810.062-0.0363-0.1957-0.13570.09070.05290.12130.00940.14680.01070.00390.187-0.0190.1172-26.288428.4108-11.9931
20.6139-0.07190.21160.5370.18760.15680.03950.0364-0.0101-0.1016-0.0808-0.0124-0.0334-0.02310.00280.0885-0.00210.00180.12420.00410.0805-23.398933.0107-2.032
30.0343-0.0053-0.02960.03430.04580.16360.0367-0.08070.0970.0228-0.05490.0375-0.0802-0.1143-0.00910.1009-0.01790.02320.17090.00770.1326-10.036632.486313.3262
40.04330.09720.06030.3401-0.03270.3080.11010.16210.1548-0.0847-0.1211-0.1837-0.01540.16550.07820.10.01490.04550.18170.05820.1617-3.833632.3324-3.9025
50.0123-0.079-0.02160.51520.15470.40710.0622-0.01990.15290.05190.0172-0.1947-0.0260.2276-0.02830.114-0.0270.0260.24840.02460.27397.389638.06267.3826
60.32690.11360.12530.37960.01880.4040.0816-0.05180.0918-0.031-0.0452-0.117-0.02940.1262-0.01910.09490.00210.02290.14180.02540.17011.922228.64398.5464
70.27890.1164-0.02150.2542-0.23710.25470.0761-0.0448-0.06020.08290.07860.06310.0647-0.0414-0.03690.1231-0.0233-0.00570.16650.04220.1161-7.706723.31420.406
80.20130.11390.15661.0480.17140.39410.0601-0.2697-0.21280.1332-0.0164-0.28650.08010.11130.00050.12390.0074-0.01240.21870.05860.21444.197220.475515.3218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 1:19
2X-RAY DIFFRACTION2chain A and resid 20:142
3X-RAY DIFFRACTION3chain A and resid 143:169
4X-RAY DIFFRACTION4chain A and resid 170:209
5X-RAY DIFFRACTION5chain A and resid 210:219
6X-RAY DIFFRACTION6chain A and resid 220:272
7X-RAY DIFFRACTION7chain A and resid 273:277
8X-RAY DIFFRACTION8chain A and resid 278:316

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