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- PDB-1tli: THERMOLYSIN (2% ISOPROPANOL SOAKED CRYSTALS) -

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Basic information

Entry
Database: PDB / ID: 1tli
TitleTHERMOLYSIN (2% ISOPROPANOL SOAKED CRYSTALS)
ComponentsTHERMOLYSIN
KeywordsHYDROLASE / METALLOPROTEINASE / ORGANIC SOLVENT
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
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / ISOMORPHOUS REPLACEMENT / Resolution: 2.05 Å
AuthorsEnglish, A.C. / Done, S.H. / Groom, C.R. / Hubbard, R.E.
CitationJournal: Proteins / Year: 1999
Title: Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol.
Authors: English, A.C. / Done, S.H. / Caves, L.S. / Groom, C.R. / Hubbard, R.E.
History
DepositionOct 27, 1998Processing site: BNL
Revision 1.0Feb 18, 2000Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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_conn.ptnr2_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

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Assembly

Deposited unit
A: THERMOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6667
Polymers34,3621
Non-polymers3046
Water2,684149
1
A: THERMOLYSIN
hetero molecules

A: THERMOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,33214
Polymers68,7252
Non-polymers60812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Unit cell
Length a, b, c (Å)93.930, 93.930, 130.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein THERMOLYSIN


Mass: 34362.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE ACTIVE SITE CLEFT OF THERMOLYSIN CONTAINS AT LEAST FOUR SUBSITES S1, S1(PRIME), S2, AND S2(PRIME).

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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: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
14.6 mMprotein11
245 %DMSO11
350 mMTris-HCl11
42.5 M11CsClpH7.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 20770 / % possible obs: 95 % / Redundancy: 7.2 % / Biso Wilson estimate: 20.79 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 5.5
Reflection shellResolution: 2.05→2.19 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2.2 / % possible all: 93
Reflection shell
*PLUS
% possible obs: 93 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT / Resolution: 2.05→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.17
Details: THIS ENTRY FORMS PART OF A SERIES OF STRUCTURES GENERATED FROM SOAKING CRYSTALS OF THERMOLYSIN IN ISOPROPANOL. AT THIS CONCENTRATION (2% ISOPROPANOL) THERE IS NO ELECTRON DENSITY ...Details: THIS ENTRY FORMS PART OF A SERIES OF STRUCTURES GENERATED FROM SOAKING CRYSTALS OF THERMOLYSIN IN ISOPROPANOL. AT THIS CONCENTRATION (2% ISOPROPANOL) THERE IS NO ELECTRON DENSITY CORRESPONDING TO THE DIPEPTIDE OBSERVED IN THE ACTIVE SITE OF THE NATIVE ENZYME.
RfactorNum. reflection% reflection
Rfree0.219 -5 %
Rwork0.1653 --
obs-19709 95 %
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2451 0 9 149 2609
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0360.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.8353
X-RAY DIFFRACTIONp_mcangle_it3.1265
X-RAY DIFFRACTIONp_scbond_it5.4735
X-RAY DIFFRACTIONp_scangle_it6.90210
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1370.15
X-RAY DIFFRACTIONp_singtor_nbd0.1820.3
X-RAY DIFFRACTIONp_multtor_nbd0.3540.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1510.3
X-RAY DIFFRACTIONp_planar_tor4.715
X-RAY DIFFRACTIONp_staggered_tor16.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor23.120
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.227 / Rfactor Rwork: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.9

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