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- PDB-6ya1: Zinc metalloprotease ProA -

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Basic information

Entry
Database: PDB / ID: 6ya1
TitleZinc metalloprotease ProA
ComponentsZinc metalloproteinase
KeywordsMETAL BINDING PROTEIN / ProA / M4 protease / TLP-like / Metalloprotease / zinc
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
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
ACETATE ION / Zinc metalloproteinase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsSchmelz, S. / Blankenfeldt, W.
CitationJournal: Cell.Microbiol. / Year: 2021
Title: Zinc metalloprotease ProA of Legionella pneumophila increases alveolar septal thickness in human lung tissue explants by collagen IV degradation.
Authors: Scheithauer, L. / Thiem, S. / Schmelz, S. / Dellmann, A. / Bussow, K. / Brouwer, R.M.H.J. / Unal, C.M. / Blankenfeldt, W. / Steinert, M.
History
DepositionMar 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 24, 2024Group: 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: Zinc metalloproteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,39412
Polymers37,7891
Non-polymers60511
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-149 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.262, 108.213, 47.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-405-

ZN

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Components

#1: Protein Zinc metalloproteinase / PEP1 / PRO A


Mass: 37788.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P21347, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 47.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M (w/v) zinc acetate and 10 % (v/v) 2 propanol in 0.1 M (w/v) sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.48→47.39 Å / Num. obs: 58912 / % possible obs: 99.5 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.033 / Rrim(I) all: 0.089 / Net I/σ(I): 14.1 / Num. measured all: 422798
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.48-1.517.51.1462133128470.6610.4421.231.698.8
8.11-47.396.10.03826534380.9980.0160.04145.699.3

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Processing

Software
NameVersionClassification
PHENIX1.18rc4refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NQX

3nqx


Resolution: 1.48→47.39 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1873 2941 5 %
Rwork0.1677 55926 -
obs0.1687 58867 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.36 Å2 / Biso mean: 22.2406 Å2 / Biso min: 8.01 Å2
Refinement stepCycle: final / Resolution: 1.48→47.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 23 334 2916
Biso mean--23.71 31.83 -
Num. residues----328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.48-1.50.25191540.25312573272798
1.5-1.530.27351280.23872625275399
1.53-1.560.25761410.23282587272899
1.56-1.590.22871470.2212631277899
1.59-1.620.2691340.21362619275399
1.62-1.660.26041170.21272614273199
1.66-1.690.2181440.20862655279999
1.69-1.740.21791280.18242624275299
1.74-1.780.1991340.19052637277199
1.78-1.840.20211700.18492612278299
1.84-1.90.19791410.180826852826100
1.9-1.960.19761360.17582619275599
1.96-2.040.19161420.17662657279999
2.04-2.130.18691360.158926672803100
2.13-2.250.17361330.15262686281999
2.25-2.390.16451330.148626842817100
2.39-2.570.15691340.152326902824100
2.57-2.830.18891530.151526902843100
2.83-3.240.14621410.163427262867100
3.24-4.080.17111530.14422742289599
4.08-47.390.19041420.162829033045100

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