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- PDB-6lzo: Thermolysin with 1,10-phenanthroline -

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Basic information

Entry
Database: PDB / ID: 6lzo
TitleThermolysin with 1,10-phenanthroline
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 ...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
1,10-PHENANTHROLINE / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

Downloads & links

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Assembly

Deposited unit
A: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,70210
Polymers34,3601
Non-polymers1,3429
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area12600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.772, 92.772, 129.103
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-716-

HOH

21A-736-

HOH

31A-743-

HOH

41A-761-

HOH

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Components

#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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-PHN / 1,10-PHENANTHROLINE


Mass: 180.205 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C12H8N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.3 %
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: 1.8→20 Å / Num. obs: 30705 / % possible obs: 99 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.024 / Rrim(I) all: 0.09 / Net I/σ(I): 34.5
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 4.233 / Num. unique obs: 1490 / Rpim(I) all: 0.142 / Rrim(I) all: 0.405 / % possible all: 98.7

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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: 1.8→19.85 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.875 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 1999 6.5 %RANDOM
Rwork0.172 ---
obs0.1746 28690 98.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85 Å2 / Biso mean: 28.41 Å2 / Biso min: 15.31 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.8→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 100 275 2807
Biso mean--54.7 40.63 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122607
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172176
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.6363554
X-RAY DIFFRACTIONr_angle_other_deg1.471.5745029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3275317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.90723.358134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54115357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7651510
X-RAY DIFFRACTIONr_chiral_restr0.0790.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023102
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02610
LS refinement shellResolution: 1.801→1.848 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 144 -
Rwork0.275 2059 -
all-2203 -
obs--97.43 %

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