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- PDB-1tlx: THERMOLYSIN (NATIVE) -

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Basic information

Entry
Database: PDB / ID: 1tlx
TitleTHERMOLYSIN (NATIVE)
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
LYSINE / VALINE / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / ISOMORPHOUS REPLACEMENT / Resolution: 2.1 Å
AuthorsEnglish, A.C. / Done, S.H. / Groom, C.R. / Hubbard, R.E.
Citation
Journal: 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.
#1: Journal: Protein Sci. / Year: 1995
Title: Structural Analysis of Zinc Substitutions in the Active Site of Thermolysin
Authors: Holland, D.R. / Hausrath, A.C. / Juers, D. / Matthews, B.W.
#2: Journal: J.Mol.Biol. / Year: 1982
Title: Structure of Thermolysin Refined at 1.6 Angstrom Resolution
Authors: Holmes, M.A. / Matthews, B.W.
History
DepositionNov 2, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Mar 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Category: entity_src_nat

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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)34,9319
Polymers34,3621
Non-polymers5688
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.910, 93.910, 131.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 1 molecules A

#1: Protein THERMOLYSIN / HYDROLASE (METALLOPROTEASE)


Mass: 34362.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin

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Non-polymers , 6 types, 154 molecules

#2: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#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: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE ACTIVE SITE CLEFT OF THERMOLYSIN CONTAINS AT LEAST FOUR SUBSITES S1, S1(PRIME), S2, AND S2(PRIME).
Nonpolymer detailsRESIDUES 317 AND 318 FORM A DIPEPTIDE (VAL-LYS) BOUND IN THE ACTIVE SITE OF THE MOLECULE. IT IS ...RESIDUES 317 AND 318 FORM A DIPEPTIDE (VAL-LYS) BOUND IN THE ACTIVE SITE OF THE MOLECULE. IT IS PRESUMED THAT THE ORIGIN OF THIS DIPEPTIDE IS THE C-TERMINAL TWO RESIDUES OF THE PROTEIN. SINCE THE C-TERMINUS APPEARS AT FULL OCCUPANCY, MOLECULES NOT INCORPORATED INTO THE CRYSTAL MUST HAVE BEEN SACRIFICED. THE NATIVE ENZYME HAS A VAL-LYS DIPEPTIDE BOUND IN THE ACTIVE SITE. IT IS PRESUMED THAT THE ORIGIN OF THIS DIPEPTIDE IS THE C-TERMINAL TWO RESIDUES OF THE PROTEIN. SINCE THE C-TERMINUS APPEARS AT FULL OCCUPANCY, MOLECULES NOT INCORPORATED INTO THE CRYSTAL MUST HAVE BEEN SACRIFICED.

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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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: unknown
Details: This particular structure is not described in this paper.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 20252 / % possible obs: 99 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 4.9
Reflection shellResolution: 2.1→2.24 Å / Redundancy: 15 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2 / % possible all: 98

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT / Resolution: 2.1→20 Å / SU B: 3.5 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.17
Details: THIS ENTRY FORMS PART OF A SERIES OF STRUCTURES GENERATED FROM SOAKING CRYSTALS OF THERMOLYSIN IN ORGANIC SOLVENTS/ SOLUTES. THIS ENTRY WAS USED AS THE INITIAL MODEL FOR THE REFINEMENT OF THESE STRUCTURES.
RfactorNum. reflection% reflection
Rfree0.214 -5 %
Rwork0.1533 --
obs-19215 99 %
Displacement parametersBiso mean: 25.18 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 26 146 2630
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0350.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.8013
X-RAY DIFFRACTIONp_mcangle_it3.075
X-RAY DIFFRACTIONp_scbond_it5.4735
X-RAY DIFFRACTIONp_scangle_it6.78610
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1360.15
X-RAY DIFFRACTIONp_singtor_nbd0.1840.3
X-RAY DIFFRACTIONp_multtor_nbd0.3520.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.140.3
X-RAY DIFFRACTIONp_planar_tor4.67
X-RAY DIFFRACTIONp_staggered_tor17.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.420
X-RAY DIFFRACTIONp_special_tor

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