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- PDB-8pz0: Intracellular leucine aminopeptidase of Pseudomonas aeruginosa PA14. -

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Basic information

Entry
Database: PDB / ID: 8pz0
TitleIntracellular leucine aminopeptidase of Pseudomonas aeruginosa PA14.
ComponentsProbable cytosol aminopeptidase
KeywordsHYDROLASE / aminopeptidase / metalloenzyme / hexamer
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 / Probable cytosol aminopeptidase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 26, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,65916
Polymers55,0571
Non-polymers60215
Water7,476415
1
A: Probable cytosol aminopeptidase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)333,95296
Polymers330,3436
Non-polymers3,60990
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area35750 Å2
ΔGint-657 kcal/mol
Surface area102680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.950, 181.950, 87.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-1032-

HOH

21A-1076-

HOH

31A-1095-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 55057.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Strain: PA14 / 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 , 5 types, 430 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 3.79 Å3/Da / Density % sol: 67.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 14 % PEG 3350 and 200 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: Dec 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→45.49 Å / Num. obs: 78846 / % possible obs: 100 % / Redundancy: 36.7 % / Biso Wilson estimate: 33.95 Å2 / CC1/2: 1 / Rrim(I) all: 0.14 / Net I/σ(I): 17.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 18.56 % / Rmerge(I) obs: 4.03 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3880 / CC1/2: 0.3 / Rrim(I) all: 4.141 / % possible all: 99.59

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
xia2data scaling
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.49 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1897 3873 4.91 %
Rwork0.1676 --
obs0.1687 78803 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→45.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3714 0 30 415 4159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073803
X-RAY DIFFRACTIONf_angle_d0.8975125
X-RAY DIFFRACTIONf_dihedral_angle_d5.875538
X-RAY DIFFRACTIONf_chiral_restr0.056591
X-RAY DIFFRACTIONf_plane_restr0.013664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.35851380.34142638X-RAY DIFFRACTION99
1.82-1.850.30751230.31872625X-RAY DIFFRACTION100
1.85-1.870.34981240.29162667X-RAY DIFFRACTION100
1.87-1.890.24931390.25932617X-RAY DIFFRACTION100
1.89-1.920.26461360.23752639X-RAY DIFFRACTION100
1.92-1.950.26131400.2262635X-RAY DIFFRACTION100
1.95-1.980.21631540.21362652X-RAY DIFFRACTION100
1.98-2.010.24191420.19262614X-RAY DIFFRACTION100
2.01-2.050.19981280.18972658X-RAY DIFFRACTION100
2.05-2.090.20771350.18332651X-RAY DIFFRACTION100
2.09-2.130.2211330.18092655X-RAY DIFFRACTION100
2.13-2.170.21531350.17472651X-RAY DIFFRACTION100
2.17-2.220.21411240.17022666X-RAY DIFFRACTION100
2.22-2.270.19311360.17222644X-RAY DIFFRACTION100
2.27-2.320.18561360.16762658X-RAY DIFFRACTION100
2.32-2.390.18731360.15832662X-RAY DIFFRACTION100
2.39-2.460.18041410.1562662X-RAY DIFFRACTION100
2.46-2.540.17821110.15932684X-RAY DIFFRACTION100
2.54-2.630.16221370.162688X-RAY DIFFRACTION100
2.63-2.730.16871580.16432661X-RAY DIFFRACTION100
2.73-2.860.20221400.16272657X-RAY DIFFRACTION100
2.86-3.010.2081580.17222688X-RAY DIFFRACTION100
3.01-3.20.16961440.16952683X-RAY DIFFRACTION100
3.2-3.440.19431410.16882699X-RAY DIFFRACTION100
3.44-3.790.20291470.16332717X-RAY DIFFRACTION100
3.79-4.340.14941360.14452747X-RAY DIFFRACTION100
4.34-5.460.15031450.14392783X-RAY DIFFRACTION100
5.46-45.490.20541560.16282929X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 58.3984 Å / Origin y: 50.4129 Å / Origin z: 36.8664 Å
111213212223313233
T0.3504 Å2-0.0112 Å20.0356 Å2-0.378 Å2-0.0271 Å2--0.3507 Å2
L0.483 °2-0.2715 °20.0425 °2-0.6485 °2-0.1727 °2--0.333 °2
S-0.0244 Å °-0.0375 Å °-0.039 Å °0.0392 Å °-0.002 Å °-0.0169 Å °0.0358 Å °-0.03 Å °0.0005 Å °
Refinement TLS groupSelection details: all

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