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- PDB-6tli: THERMOLYSIN (60% ISOPROPANOL SOAKED CRYSTALS) -

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Basic information

Entry
Database: PDB / ID: 6tli
TitleTHERMOLYSIN (60% ISOPROPANOL SOAKED CRYSTALS)
ComponentsPROTEIN (THERMOLYSIN)
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 / Thermolysin metallopeptidase, alpha-helical 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
ISOPROPYL ALCOHOL / 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.
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 29, 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_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_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: PROTEIN (THERMOLYSIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,84610
Polymers34,3621
Non-polymers4849
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.120, 94.120, 130.680
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 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

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Non-polymers , 5 types, 130 molecules

#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 / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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 detailsTHE ORIENTATION OF ISOPROPANOL IPA 1003 IS TENTATIVE. ALTHOUGH THE DENSITY FOR IPA 1003 IS STRONG, ...THE ORIENTATION OF ISOPROPANOL IPA 1003 IS TENTATIVE. ALTHOUGH THE DENSITY FOR IPA 1003 IS STRONG, THE ORIENTATION OF THE MOLECULE WITHIN THE DENSITY IS AMBIGUOUS.

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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: 49.4 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.6 mMTLN11
245 %DMSO11
350 mMTris-HCl11
42.5 M11CsCl

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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: May 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 20404 / % possible obs: 99 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 5.2
Reflection shellResolution: 2.1→2.24 Å / Redundancy: 8 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 1.9 / % possible all: 98
Reflection shell
*PLUS
% possible obs: 98 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
CCP4data scaling
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT / Resolution: 2.1→30 Å / SU B: 3.85 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.18
Details: THIS ENTRY FORMS PART OF A SERIES OF STRUCTURES GENERATED FROM SOAKING CRYSTALS OF THERMOLYSIN IN ISOPROPANOL. AT THIS CONCENTRATION (25% ISOPROPANOL) TWO MOLECULES OF ISOPROPANOL ARE ...Details: THIS ENTRY FORMS PART OF A SERIES OF STRUCTURES GENERATED FROM SOAKING CRYSTALS OF THERMOLYSIN IN ISOPROPANOL. AT THIS CONCENTRATION (25% ISOPROPANOL) TWO MOLECULES OF ISOPROPANOL ARE PROTEIN BOUND. ONE MOLECULE OF ISOPROPANOL IS LOCATED IN THE S1(PRIME) SUBSITE.
RfactorNum. reflection% reflection
Rfree0.222 -5 %
Rwork0.168 --
obs-18843 97 %
Displacement parametersBiso mean: 25.63 Å2 / Baniso 23: 0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 9 133 2594
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_d0.0450.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.7473
X-RAY DIFFRACTIONp_mcangle_it3.1735
X-RAY DIFFRACTIONp_scbond_it5.6165
X-RAY DIFFRACTIONp_scangle_it6.99310
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1320.15
X-RAY DIFFRACTIONp_singtor_nbd0.1810.3
X-RAY DIFFRACTIONp_multtor_nbd0.3480.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.150.3
X-RAY DIFFRACTIONp_planar_tor4.77
X-RAY DIFFRACTIONp_staggered_tor17.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.820
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg20.04

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