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- PDB-9nlo: Escherichia coli Signal Peptidase I Delta 2-76 P84A in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9nlo
TitleEscherichia coli Signal Peptidase I Delta 2-76 P84A in complex with lipopeptide inhibitor
Components
  • ARYLOMYCIN A2
  • Signal peptidase I
KeywordsHYDROLASE/INHIBITOR / Signal Peptidase / Membrane Protein / Serine-Lysine catalytic Dyad / Inhibitor complex / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


signal peptidase I / : / protein processing / peptidase activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / plasma membrane
Similarity search - Function
Signal peptidase I, all-beta subdomain / Peptidase S26A, signal peptidase I, lysine active site / Signal peptidases I lysine active site. / Peptidase S26A, signal peptidase I / Signal peptidase, peptidase S26 / Peptidase S26A, signal peptidase I, conserved site / Signal peptidases I signature 3. / Peptidase S26A, signal peptidase I, serine active site / Signal peptidases I serine active site. / Peptidase S26 / LexA/Signal peptidase-like superfamily
Similarity search - Domain/homology
ARYLOMYCIN A2 / 10-METHYLUNDECANOIC ACID / Signal peptidase I
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsPaetzel, M. / Luo, C.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Citation
Journal: J.Struct.Biol. / Year: 2025
Title: Crystal structure of Escherichia coli type I signal peptidase P84A in complex with lipopeptide antibiotic arylomycin A 2 .
Authors: Luo, C. / Paetzel, M.
#1: Journal: J Biol Chem / Year: 2004
Title: Crystallographic and biophysical analysis of a bacterial signal peptidase in complex with a lipopeptide-based inhibitor.
Authors: Paetzel, M. / Goodall, J.J. / Kania, M. / Dalbey, R.E. / Page, M.G.
#2: Journal: Biochemistry / Year: 2009
Title: Crystallographic analysis of bacterial signal peptidase in ternary complex with arylomycin A2 and a beta-sultam inhibitor.
Authors: Luo, C. / Roussel, P. / Dreier, J. / Page, M.G. / Paetzel, M.
History
DepositionMar 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_last ..._citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Signal peptidase I
B: Signal peptidase I
C: ARYLOMYCIN A2
D: ARYLOMYCIN A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6958
Polymers57,1714
Non-polymers5254
Water2,234124
1
A: Signal peptidase I
D: ARYLOMYCIN A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8484
Polymers28,5852
Non-polymers2622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-1 kcal/mol
Surface area11310 Å2
MethodPISA
2
B: Signal peptidase I
C: ARYLOMYCIN A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8484
Polymers28,5852
Non-polymers2622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-0 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.800, 71.800, 263.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Signal peptidase I / SPase I / Leader peptidase I


Mass: 27940.621 Da / Num. of mol.: 2 / Mutation: P84A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: lepB, b2568, JW2552 / Plasmid: pET3d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00803, signal peptidase I
#2: Protein/peptide ARYLOMYCIN A2


Type: Lipopeptide / Class: Antibiotic / Mass: 644.674 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: ARYLOMYCIN A2 IS A BIARYL-BRIDGED LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) N-TERM EXOCYCLIC TRIPEPTIDE (2) A TRICYCLIC PEPTIDE, WITH [3,3] BIARYL BOND BETWEEN RESIDUE 4 AND 6 AN ...Details: ARYLOMYCIN A2 IS A BIARYL-BRIDGED LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) N-TERM EXOCYCLIC TRIPEPTIDE (2) A TRICYCLIC PEPTIDE, WITH [3,3] BIARYL BOND BETWEEN RESIDUE 4 AND 6 AN ISO-C12 FATTY ACID IS LINKED TO RESIDUE 1.
Source: (synth.) SYNTHETIC CONSTRUCT (others) / References: ARYLOMYCIN A2
#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-M12 / 10-METHYLUNDECANOIC ACID


Type: Lipopeptide / Class: Antibiotic / Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
Details: ARYLOMYCIN A2 IS A BIARYL-BRIDGED LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) N-TERM EXOCYCLIC TRIPEPTIDE (2) A TRICYCLIC PEPTIDE, WITH [3,3] BIARYL BOND BETWEEN RESIDUE 4 AND 6 AN ...Details: ARYLOMYCIN A2 IS A BIARYL-BRIDGED LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) N-TERM EXOCYCLIC TRIPEPTIDE (2) A TRICYCLIC PEPTIDE, WITH [3,3] BIARYL BOND BETWEEN RESIDUE 4 AND 6 AN ISO-C12 FATTY ACID IS LINKED TO RESIDUE 1.
Feature type: SUBJECT OF INVESTIGATION / References: ARYLOMYCIN A2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Compound detailsARYLOMYCIN A2 IS A CYCLIC LIPOHEXAPEPTIDE, A MEMBER OF THE ARYLOMYCIN FAMILY. ALL MEMBERS HAVE A ...ARYLOMYCIN A2 IS A CYCLIC LIPOHEXAPEPTIDE, A MEMBER OF THE ARYLOMYCIN FAMILY. ALL MEMBERS HAVE A FATTY ACID AT THE N-TERM AND A CORE STRUCTURE OF TRIPEPTIDE MACROCYCLE FORMED BY A C-C BIARYL LINKAGE BETWEEN RESIDUES 4 AND 6. HERE, ARYLOMYCIN A2 IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND ONE LIGAND (HET) M12.
Has ligand of interestY
Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 59.5 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 25%v/v PEG 4000, 0.05M NH4OAC, 0.1M NaOAc pH 4.6, 0.033M L-proline

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.1047 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1047 Å / Relative weight: 1
ReflectionResolution: 2.32→52.63 Å / Num. obs: 30863 / % possible obs: 99.7 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.039 / Rrim(I) all: 0.105 / Net I/σ(I): 13
Reflection shellResolution: 2.32→2.45 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 4381 / Rpim(I) all: 0.154 / Rrim(I) all: 0.422 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→35.596 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.326 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.195
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2338 1119 3.643 %
Rwork0.2086 29597 -
all0.21 --
obs-30716 99.266 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.583 Å2
Baniso -1Baniso -2Baniso -3
1-0.545 Å2-0 Å2-0 Å2
2--0.545 Å2-0 Å2
3----1.091 Å2
Refinement stepCycle: LAST / Resolution: 2.32→35.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3478 0 124 124 3726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0123692
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163387
X-RAY DIFFRACTIONr_angle_refined_deg1.41.8495015
X-RAY DIFFRACTIONr_angle_other_deg0.4751.7847793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2455448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.448521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4910526
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.44610154
X-RAY DIFFRACTIONr_chiral_restr0.0640.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024346
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02840
X-RAY DIFFRACTIONr_nbd_refined0.1850.2516
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.23078
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21751
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21931
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2155
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0630.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1330.212
X-RAY DIFFRACTIONr_nbd_other0.1390.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1140.23
X-RAY DIFFRACTIONr_mcbond_it3.6064.521811
X-RAY DIFFRACTIONr_mcbond_other3.6034.521811
X-RAY DIFFRACTIONr_mcangle_it5.5118.0912252
X-RAY DIFFRACTIONr_mcangle_other5.5098.0912253
X-RAY DIFFRACTIONr_scbond_it3.7864.7891881
X-RAY DIFFRACTIONr_scbond_other3.7854.791882
X-RAY DIFFRACTIONr_scangle_it5.9398.6872763
X-RAY DIFFRACTIONr_scangle_other5.9388.6872764
X-RAY DIFFRACTIONr_lrange_it7.90842.9433775
X-RAY DIFFRACTIONr_lrange_other7.91142.973763
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.32-2.380.341740.23521070.23921950.9250.96199.36220.235
2.38-2.4450.27820.22720800.22921810.9510.96699.12880.227
2.445-2.5150.29800.21620140.21821080.9340.9799.33590.216
2.515-2.5920.29600.21619940.21820650.9470.9799.46730.216
2.592-2.6770.202770.20319350.20320180.9730.97599.70270.203
2.677-2.770.235750.18618470.18819320.9670.97999.48240.186
2.77-2.8740.197590.20618120.20518780.9790.97699.62730.206
2.874-2.9910.222600.19317370.19418030.9740.97799.66720.193
2.991-3.1230.253610.20916720.2117360.9510.97299.82720.209
3.123-3.2740.258740.21316060.21516830.9560.97299.82170.213
3.274-3.450.203690.20914930.20915650.9730.97499.80830.209
3.45-3.6570.232570.21414660.21515270.9650.97299.73810.214
3.657-3.9060.272490.21613770.21814280.9560.97199.85990.216
3.906-4.2150.201440.18412980.18413450.9760.9899.7770.184
4.215-4.6110.221480.17211850.17412360.9720.98399.75730.172
4.611-5.1440.146350.16611050.16611460.9860.98399.47640.166
5.144-5.9190.252400.2189700.2210120.9570.97199.80240.218
5.919-7.20.207390.2568500.2538920.9630.96399.66370.256
7.2-9.980.234220.2296720.2297120.9520.96697.47190.229
9.98-35.5960.401140.3523770.3544670.8590.91283.72590.352

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