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

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Basic information

Entry
Database: PDB / ID: 8pzm
TitleIntracellular leucine aminopeptidase of Pseudomonas aeruginosa PA14 bound to bestatin inhibitor and manganese
ComponentsProbable cytosol aminopeptidase
KeywordsHYDROLASE / aminopeptidase / metalloenzyme / hexamer / bestatin / inhibitor / 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 / Chem-BES / : / Probable cytosol aminopeptidase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

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Assembly

Deposited unit
A: Probable cytosol aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6617
Polymers55,0571
Non-polymers6036
Water9,548530
1
A: Probable cytosol aminopeptidase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)333,96442
Polymers330,3436
Non-polymers3,62036
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 area31660 Å2
ΔGint-75 kcal/mol
Surface area100580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.050, 182.050, 87.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-1108-

HOH

21A-1184-

HOH

31A-1189-

HOH

41A-1198-

HOH

51A-1227-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable cytosol aminopeptidase


Mass: 55057.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Gene: pepA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02RY8

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Non-polymers , 5 types, 536 molecules

#2: Chemical ChemComp-BES / 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID / BESTATIN


Mass: 308.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 530 / 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: 3.6 Å3/Da / Density % sol: 69.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 5 mM MnCl2, 20 % PEG 3350, 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: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.7→43.79 Å / Num. obs: 93600 / % possible obs: 100 % / Redundancy: 40.3 % / CC1/2: 1 / Rrim(I) all: 0.272 / Net I/σ(I): 13.3
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 4607 / CC1/2: 0.3 / Rrim(I) all: 5.652

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→43.78 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.189 4725 5.05 %RANDOM
Rwork0.1696 ---
obs0.1706 93542 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3703 0 36 530 4269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073800
X-RAY DIFFRACTIONf_angle_d0.9015122
X-RAY DIFFRACTIONf_dihedral_angle_d6.044536
X-RAY DIFFRACTIONf_chiral_restr0.055592
X-RAY DIFFRACTIONf_plane_restr0.013664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.31531490.31392922X-RAY DIFFRACTION100
1.72-1.740.3221620.30622891X-RAY DIFFRACTION100
1.74-1.760.28331500.29582928X-RAY DIFFRACTION100
1.76-1.780.30231610.30172908X-RAY DIFFRACTION100
1.78-1.810.3231490.31862930X-RAY DIFFRACTION100
1.81-1.830.2961560.28752904X-RAY DIFFRACTION100
1.83-1.860.31621400.28962965X-RAY DIFFRACTION100
1.86-1.890.31131500.24372921X-RAY DIFFRACTION100
1.89-1.910.25011610.23232923X-RAY DIFFRACTION100
1.91-1.950.21011640.21092929X-RAY DIFFRACTION100
1.95-1.980.22611540.19622921X-RAY DIFFRACTION100
1.98-2.020.21111770.18732905X-RAY DIFFRACTION100
2.02-2.050.23121560.18452926X-RAY DIFFRACTION100
2.05-2.10.18261670.17842928X-RAY DIFFRACTION100
2.1-2.140.18311510.17472964X-RAY DIFFRACTION100
2.14-2.190.16441690.16842926X-RAY DIFFRACTION100
2.19-2.250.18031640.16372940X-RAY DIFFRACTION100
2.25-2.310.18411580.16682943X-RAY DIFFRACTION100
2.31-2.380.20251370.16022976X-RAY DIFFRACTION100
2.38-2.450.2111710.16252923X-RAY DIFFRACTION100
2.45-2.540.1831560.16092958X-RAY DIFFRACTION100
2.54-2.640.21291480.16042975X-RAY DIFFRACTION100
2.64-2.760.18311480.16412977X-RAY DIFFRACTION100
2.76-2.910.19581620.16822977X-RAY DIFFRACTION100
2.91-3.090.17511440.16462995X-RAY DIFFRACTION100
3.09-3.330.16661590.16252998X-RAY DIFFRACTION100
3.33-3.660.20381650.163015X-RAY DIFFRACTION100
3.66-4.190.16111590.14373035X-RAY DIFFRACTION100
4.19-5.280.14161450.13133085X-RAY DIFFRACTION100
5.28-43.780.16011930.15613229X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 58.856 Å / Origin y: 50.5455 Å / Origin z: 36.8031 Å
111213212223313233
T0.2057 Å2-0.0097 Å20.0258 Å2-0.2197 Å2-0.017 Å2--0.1323 Å2
L0.7855 °2-0.4156 °20.1528 °2-0.5241 °2-0.155 °2--0.2145 °2
S-0.0239 Å °-0.0684 Å °-0.0236 Å °0.0459 Å °0.0112 Å °0.0654 Å °-0.001 Å °-0.0769 Å °0.0131 Å °
Refinement TLS groupSelection details: all

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