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- PDB-8acr: Structure of Pseudomonas aeruginosa aminopeptidase, PaAP -

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Basic information

Entry
Database: PDB / ID: 8acr
TitleStructure of Pseudomonas aeruginosa aminopeptidase, PaAP
ComponentsKeratinase KP1
KeywordsHYDROLASE / E340A mutant / Full-length
Function / homology
Function and homology information


metalloexopeptidase activity / aminopeptidase activity / proteolysis
Similarity search - Function
Peptidase M28, SGAP-like / Peptidase M28 family / PA domain superfamily / PA domain / PA domain / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHarding, C.J. / Czekster, C.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: An anti-biofilm cyclic peptide targets a secreted aminopeptidase from P. aeruginosa.
Authors: Harding, C.J. / Bischoff, M. / Bergkessel, M. / Czekster, C.M.
History
DepositionJul 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Keratinase KP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1025
Polymers54,8831
Non-polymers2194
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-125 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.017, 90.642, 129.718
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Keratinase KP1


Mass: 54882.883 Da / Num. of mol.: 1 / Mutation: E340A
Source method: isolated from a genetically manipulated source
Details: Truncation construct / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: E3ULB5
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MMT (DL-Malic acid, MES monohydrate, Tris) pH 6.0, 25 % w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9 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: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→52.75 Å / Num. obs: 32511 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 47.07 Å2 / Rpim(I) all: 0.016 / Rrim(I) all: 0.059 / Net I/σ(I): 21.7 / Num. measured all: 428078
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.1-2.141111681015230.1640.55396.9
5.7-52.7611.975.42140917940.0090.032100

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Processing

Software
NameVersionClassification
xia23.8.1data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AC7

8ac7


Resolution: 2.1→46.017 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.224 1579 4.87 %
Rwork0.1753 30854 -
obs0.1775 32433 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.99 Å2 / Biso mean: 55.3543 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.1→46.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3681 0 4 194 3879
Biso mean--52.85 56.16 -
Num. residues----486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.16760.31621570.2545267998
2.1676-2.2450.26871410.22272721100
2.245-2.33490.26461520.21052792100
2.3349-2.44120.26261210.20672800100
2.4412-2.56990.26091410.21452772100
2.5699-2.73090.2951350.21662795100
2.7309-2.94170.2611560.20712779100
2.9417-3.23760.23511540.20682813100
3.2376-3.7060.25961460.18462810100
3.706-4.66840.16831410.1432882100
4.6684-46.0170.19031350.14763011100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4275-0.01230.00791.58530.45440.1169-0.0941-0.09950.2190.0356-0.05820.3469-0.1153-0.02450.00070.34760.08580.04250.4081-0.03990.4764-7.614311.374221.0858
21.2627-0.01840.4330.6886-0.62220.702-0.2675-0.56160.06430.26840.0589-0.2452-0.2422-0.0679-0.0010.69890.0803-0.06160.6238-0.02380.479619.0218-11.370144.8687
31.4654-0.2103-0.00140.29030.21341.3080.056-0.0081-0.01290.21220.06680.00930.28960.11240.00050.44840.11130.00270.3939-0.02270.41313.979-0.351520.9714
40.6122-0.3116-0.16050.3058-0.17690.3961-0.03960.1335-0.44730.08290.0545-0.06070.02790.3850.00010.71080.1209-0.0020.5487-0.03540.61057.214-12.593718.7304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 106 )A36 - 106
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 260 )A107 - 260
3X-RAY DIFFRACTION3chain 'A' and (resid 261 through 496 )A261 - 496
4X-RAY DIFFRACTION4chain 'A' and (resid 497 through 536 )A497 - 536

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