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- PDB-6lzn: Thermolysin -

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Basic information

Entry
Database: PDB / ID: 6lzn
TitleThermolysin
ComponentsThermolysin
KeywordsHYDROLASE / Thermolysin / metalloproteinase
Function / homology
Function and homology information


thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
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 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
ISOLEUCINE / LYSINE / N-PROPANOL / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017R1D1A1B03033087 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029736 Korea, Republic Of
CitationJournal: J.Inorg.Biochem. / Year: 2021
Title: Structural analysis of metal chelation of the metalloproteinase thermolysin by 1,10-phenanthroline.
Authors: Nam, K.H.
History
DepositionFeb 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)34,9779
Polymers34,3601
Non-polymers6168
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-40 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.663, 92.663, 128.591
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1715-

HOH

21A-1737-

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 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin

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Non-polymers , 7 types, 275 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ILE / ISOLEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#7: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Tris-HCl, glycerol, Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 51659 / % possible obs: 97.9 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.036 / Rrim(I) all: 0.118 / Net I/σ(I): 40.72
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.25 / Num. unique obs: 2137 / Rpim(I) all: 0.175 / Rrim(I) all: 0.384 / % possible all: 82.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IG7

6ig7


Resolution: 1.5→19.83 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.113 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.065
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1803 2000 3.9 %RANDOM
Rwork0.1568 ---
obs0.1577 49674 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68 Å2 / Biso mean: 15.744 Å2 / Biso min: 8.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å2-0 Å2
2---0.18 Å20 Å2
3---0.58 Å2
Refinement stepCycle: final / Resolution: 1.5→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 14 267 2731
Biso mean--21.78 28.23 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132556
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172184
X-RAY DIFFRACTIONr_angle_refined_deg1.9951.6443484
X-RAY DIFFRACTIONr_angle_other_deg1.7051.5785074
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9445328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.01523.456136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07915371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6741510
X-RAY DIFFRACTIONr_chiral_restr0.1120.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022999
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02563
LS refinement shellResolution: 1.5→1.538 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.263 124 -
Rwork0.237 3087 -
obs--83.97 %

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