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- PDB-8pzy: Intracellular leucine aminopeptidase of Pseudomonas aeruginosa PA... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8pzy
TitleIntracellular leucine aminopeptidase of Pseudomonas aeruginosa PA14 - hexameric assembly with manganese bound
ComponentsProbable cytosol aminopeptidase
KeywordsHYDROLASE / aminopeptidase / metalloenzyme / hexamer / manganese
Function / homology
Function and homology information


bacterial leucyl aminopeptidase / leucyl aminopeptidase / metalloaminopeptidase activity / manganese ion binding / proteolysis / cytoplasm
Similarity search - Function
Peptidase M17, leucyl aminopeptidase, N-terminal / Cytosol aminopeptidase family, N-terminal domain / Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Macro domain-like
Similarity search - Domain/homology
BICARBONATE ION / : / AMMONIUM ION / NITRATE ION / 2-[3-[3-(2-hydroxyethoxy)propoxy]propoxy]ethanol / Probable cytosol aminopeptidase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSimpson, M.C. / Czekster, C.M. / Harding, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust210486/Z/18/Z United Kingdom
CitationJournal: Biochemistry / Year: 2023
Title: Unveiling the Catalytic Mechanism of a Processive Metalloaminopeptidase.
Authors: Simpson, M.C. / Harding, C.J. / Czekster, R.M. / Remmel, L. / Bode, B.E. / Czekster, C.M.
History
DepositionJul 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable cytosol aminopeptidase
B: Probable cytosol aminopeptidase
C: Probable cytosol aminopeptidase
D: Probable cytosol aminopeptidase
E: Probable cytosol aminopeptidase
F: Probable cytosol aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,54951
Polymers330,3436
Non-polymers2,20645
Water40,5162249
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28610 Å2
ΔGint-110 kcal/mol
Surface area103530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.530, 183.030, 316.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Probable cytosol aminopeptidase / Leucine aminopeptidase / LAP / Leucyl aminopeptidase


Mass: 55057.242 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Gene: pepA, PA14_14470 / Plasmid: pJ411 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q02RY8, leucyl aminopeptidase, bacterial leucyl aminopeptidase

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Non-polymers , 8 types, 2294 molecules

#2: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: H4N
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-P03 / 2-[3-[3-(2-hydroxyethoxy)propoxy]propoxy]ethanol


Mass: 222.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O5
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2249 / 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: 3.84 Å3/Da / Density % sol: 67.95 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5 mM MnCl2 in 20 % PEG 3350, and 172 mM ammonium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.97→54.25 Å / Num. obs: 357632 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 1 / Rrim(I) all: 0.153 / Net I/σ(I): 10.4
Reflection shellResolution: 1.97→2 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 17692 / CC1/2: 0.3 / Rrim(I) all: 3.792 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→52.75 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 17937 5.02 %
Rwork0.1764 --
obs0.1778 357297 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→52.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22212 0 110 2249 24571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822708
X-RAY DIFFRACTIONf_angle_d0.96530613
X-RAY DIFFRACTIONf_dihedral_angle_d6.7373221
X-RAY DIFFRACTIONf_chiral_restr0.0533538
X-RAY DIFFRACTIONf_plane_restr0.013969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-1.990.40255800.382211295X-RAY DIFFRACTION100
1.99-2.020.3575780.344511167X-RAY DIFFRACTION100
2.02-2.040.35755750.329811238X-RAY DIFFRACTION100
2.04-2.070.32075800.301311255X-RAY DIFFRACTION100
2.07-2.090.32576000.291211213X-RAY DIFFRACTION100
2.09-2.120.29266150.267111149X-RAY DIFFRACTION100
2.12-2.150.29115950.257311226X-RAY DIFFRACTION100
2.15-2.180.27655940.245811289X-RAY DIFFRACTION100
2.18-2.220.28016120.245511151X-RAY DIFFRACTION100
2.22-2.260.28285950.247711285X-RAY DIFFRACTION100
2.26-2.290.27795980.228911229X-RAY DIFFRACTION100
2.29-2.340.23935970.211111213X-RAY DIFFRACTION100
2.34-2.380.25035830.203911311X-RAY DIFFRACTION100
2.38-2.430.24235990.185511267X-RAY DIFFRACTION100
2.43-2.480.22366280.188311189X-RAY DIFFRACTION100
2.48-2.540.21576050.181211270X-RAY DIFFRACTION100
2.54-2.60.21465950.179211262X-RAY DIFFRACTION100
2.6-2.670.22465630.173211323X-RAY DIFFRACTION100
2.67-2.750.21085940.180711302X-RAY DIFFRACTION100
2.75-2.840.23265970.190611284X-RAY DIFFRACTION100
2.84-2.940.21976140.180411331X-RAY DIFFRACTION100
2.94-3.060.20785930.173611301X-RAY DIFFRACTION100
3.06-3.20.20326000.172311312X-RAY DIFFRACTION100
3.2-3.370.20866030.184811391X-RAY DIFFRACTION100
3.37-3.580.19476370.171111305X-RAY DIFFRACTION100
3.58-3.860.18546060.15811405X-RAY DIFFRACTION100
3.86-4.240.15765860.1411443X-RAY DIFFRACTION100
4.24-4.860.14825720.12611538X-RAY DIFFRACTION100
4.86-6.120.15866080.144411573X-RAY DIFFRACTION100
6.12-52.750.17816350.159411843X-RAY DIFFRACTION99

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