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- PDB-8ac9: Structure of Pseudomonas aeruginosa aminopeptidase, PaAP_T -

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Basic information

Entry
Database: PDB / ID: 8ac9
TitleStructure of Pseudomonas aeruginosa aminopeptidase, PaAP_T
ComponentsKeratinase KP1
KeywordsHYDROLASE / WT / Truncation
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: 2.351 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 5, 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
B: Keratinase KP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,7019
Polymers105,2432
Non-polymers4587
Water2,810156
1
A: Keratinase KP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8835
Polymers52,6211
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Keratinase KP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8184
Polymers52,6211
Non-polymers1963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.997, 52.502, 114.383
Angle α, β, γ (deg.)90.000, 95.760, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and resid 48 through 516)

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 48 - 516 / Label seq-ID: 22 - 490

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2(chain B and resid 48 through 516)BB

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Components

#1: Protein Keratinase KP1


Mass: 52621.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.5, 70 % v/v MPD

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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: 2.35→66.73 Å / Num. obs: 38179 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 41.76 Å2 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Net I/σ(I): 19.2 / Num. measured all: 256358
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.35-2.394.92.6887017950.2040.46792.6
6.38-66.756.549.81310820260.0170.042100

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Processing

Software
NameVersionClassification
xia23.6.1data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AC7

8ac7


Resolution: 2.351→48.045 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 1861 4.88 %
Rwork0.1822 36243 -
obs0.1848 38104 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.48 Å2 / Biso mean: 56.3982 Å2 / Biso min: 21.77 Å2
Refinement stepCycle: final / Resolution: 2.351→48.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7115 0 7 156 7278
Biso mean--59.23 49.6 -
Num. residues----942
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2838X-RAY DIFFRACTION3.671TORSIONAL
12B2838X-RAY DIFFRACTION3.671TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.351-2.41430.33291480.215259894
2.4143-2.48530.3011180.20692813100
2.4853-2.56550.29021420.20022767100
2.5655-2.65720.28821180.19612822100
2.6572-2.76360.28851540.18362770100
2.7636-2.88930.24141550.19252761100
2.8893-3.04160.24261380.19192765100
3.0416-3.23220.26161350.19572823100
3.2322-3.48170.22411550.18622800100
3.4817-3.83190.21371450.17242794100
3.8319-4.38610.22361590.15412815100
4.3861-5.52470.19751400.17122825100
5.5247-48.0450.22151540.194289099
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)
12.3442-0.3012-1.04022.13550.33481.0669-0.22060.86680.017-0.57970.15960.1008-0.17790.20820.04480.5275-0.1589-0.03740.59590.02170.36543.3304-7.377129.5724
21.5276-0.37790.84861.8158-1.8043.0375-0.210.16470.16050.2147-0.0149-0.0909-0.18630.51050.22390.41340.0003-0.01740.3646-0.0070.327125.9441-2.702763.7165
33.3805-1.04210.60614.13260.27993.3102-0.12340.09270.19340.3088-0.13270.1257-0.24370.04360.31750.4939-0.0398-0.02950.32610.00590.333723.4395-1.432270.2373
43.50130.16461.82021.0864-0.34632.2607-0.38330.32930.6785-0.08140.03950.1586-0.33180.22850.27840.3524-0.0386-0.03580.32230.02110.35043.6279-0.788442.5274
51.302-0.81470.11441.0796-0.58970.57-0.1628-0.3154-0.16660.23310.24770.37060.0596-0.2115-0.0890.4149-0.01690.01990.46420.0240.5399-11.4376-7.242644.7483
61.7862-0.0357-0.98652.2846-0.03561.30490.1342-0.6212-0.00270.4717-0.1633-0.0380.3196-0.36560.03430.4728-0.06110.00530.3741-0.0040.255-47.4085-9.056128.4548
73.1676-0.81540.28171.11330.07882.09090.36141.0579-0.0095-0.3607-0.46110.37340.0289-0.626-0.04410.56740.1575-0.01520.8071-0.05010.4821-69.827-1.9136-6.6321
81.1969-0.51940.1051.6933-0.10354.66910.65772.09671.3405-0.5798-0.9264-0.54090.0449-0.51570.09530.6730.30610.09771.16150.16070.5434-66.98690.4282-12.6853
92.11590.07740.19021.04930.96832.355-0.0390.15430.2647-0.0788-0.12990.0284-0.1993-0.38740.1920.2909-0.0167-0.020.28250.02150.2705-48.896-1.058715.2947
101.75570.77220.04390.59480.82991.76120.00080.2286-0.1137-0.09030.13-0.27690.10070.2011-0.11740.33510.00080.01680.29780.00050.3542-33.3307-6.216512.4466
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 105 )A48 - 105
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 188 )A106 - 188
3X-RAY DIFFRACTION3chain 'A' and (resid 189 through 255 )A189 - 255
4X-RAY DIFFRACTION4chain 'A' and (resid 256 through 381 )A256 - 381
5X-RAY DIFFRACTION5chain 'A' and (resid 382 through 516 )A382 - 516
6X-RAY DIFFRACTION6chain 'B' and (resid 44 through 105 )B44 - 105
7X-RAY DIFFRACTION7chain 'B' and (resid 106 through 188 )B106 - 188
8X-RAY DIFFRACTION8chain 'B' and (resid 189 through 255 )B189 - 255
9X-RAY DIFFRACTION9chain 'B' and (resid 256 through 381 )B256 - 381
10X-RAY DIFFRACTION10chain 'B' and (resid 382 through 516 )B382 - 516

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