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- PDB-6yze: Zinc metalloprotease ProA from native source -

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Basic information

Entry
Database: PDB / ID: 6yze
TitleZinc metalloprotease ProA from native source
ComponentsZinc metalloproteinase
KeywordsHYDROLASE / ProA / M4 protease / TLP-like / Metalloprotease / zinc / METAL BINDING PROTEIN
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
Zinc metalloproteinase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.18 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
DepositionMay 6, 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)37,8542
Polymers37,7891
Non-polymers651
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-32 kcal/mol
Surface area13750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.633, 54.604, 134.519
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 natural source / Source: (natural) Legionella pneumophila (bacteria)
References: UniProt: P21347, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 16 mg/ml native ProA 1 M sodium acetate pH 4.5 and 1.2 M tri-sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.18→50.59 Å / Num. obs: 16137 / % possible obs: 98.5 % / Redundancy: 5.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.066 / Rrim(I) all: 0.153 / Net I/σ(I): 9.7 / Num. measured all: 82983 / Scaling rejects: 6
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
2.18-2.293.90.528812921060.80.2830.6032.591.4
6.88-50.595.10.04829865910.9980.0230.05421.698.4

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Processing

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

3nqx


Resolution: 2.18→38.9 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.73
RfactorNum. reflection% reflection
Rfree0.2659 785 4.88 %
Rwork0.205 --
obs0.208 16085 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.31 Å2 / Biso mean: 25.0782 Å2 / Biso min: 8.36 Å2
Refinement stepCycle: final / Resolution: 2.18→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 1 125 2701
Biso mean--30.91 27.05 -
Num. residues----328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.18-2.310.35391200.24942323244392
2.31-2.490.34271360.24622490262698
2.49-2.740.31031410.231925602701100
2.74-3.140.26171230.219525822705100
3.14-3.950.24371310.175526012732100
3.95-38.90.21421340.186227442878100

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