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- PDB-1zdp: Crystal Structure Analysis of Thermolysin Complexed with the Inhi... -

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Basic information

Entry
Database: PDB / ID: 1zdp
TitleCrystal Structure Analysis of Thermolysin Complexed with the Inhibitor (S)-thiorphan
ComponentsThermolysin
KeywordsHYDROLASE / enzyme-inhibitor complex / zinc endopeptidase / gamma turn / thermostable
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
(2-MERCAPTOMETHYL-3-PHENYL-PROPIONYL)-GLYCINE / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsRoderick, S.L. / Fournie-Zaluski, M.C. / Roques, B.P. / Matthews, B.W.
CitationJournal: Biochemistry / Year: 1989
Title: Thiorphan and retro-thiorphan display equivalent interactions when bound to crystalline thermolysin
Authors: Roderick, S.L. / Fournie-Zaluski, M.C. / Roques, B.P. / Matthews, B.W.
History
DepositionApr 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 23, 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_ref_seq_dif / 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_ref_seq_dif.details / _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
E: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8417
Polymers34,3621
Non-polymers4796
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.000, 94.000, 132.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Cell settinghexagonal
Space group name H-MP6122
DetailsThe enzyme acts as a monomer.

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Components

#1: Protein Thermolysin / E.C.3.4.24.27 / Thermostable neutral proteinase


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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-TIO / (2-MERCAPTOMETHYL-3-PHENYL-PROPIONYL)-GLYCINE / THIORPHAN


Mass: 253.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15NO3S / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.43 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 277 K / Method: dilution with h2o / pH: 7.2
Details: Tris acetate, calcium acetate, DMSO, pH 7.20, dilution with H2O, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: KODAK / Detector: FILM / Date: 1987 / Details: GRAPHITE MONOCHROMATOR, COLLIMATING SLITS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 26142 / % possible obs: 68 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.038

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Processing

Software
NameVersionClassification
OSCTSTdata collection
ROTAVATAdata reduction
TNTrefinement
OSCTSTdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3TLN

3tln
PDB Unreleased entry


Resolution: 1.7→10 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: NONE / σ(F): 0 / Stereochemistry target values: TNT VERSION 1.0 / Details: 35 CYCLES OF CONJUGATE GRADIENT REFINEMENT
RfactorNum. reflection% reflection
Rwork0.183 --
all0.183 25988 -
obs0.183 25988 68 %
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 22 161 2615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONt_bond_d0.022508
X-RAY DIFFRACTIONt_angle_deg3.533405
X-RAY DIFFRACTIONt_dihedral_angle_d16.7121440
X-RAY DIFFRACTIONt_trig_c_planes0.01367
X-RAY DIFFRACTIONt_gen_planes0.015376
X-RAY DIFFRACTIONt_it4.2282491
X-RAY DIFFRACTIONt_nbd0.06213
X-RAY DIFFRACTIONt_incorr_chiral_ct0

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