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- PDB-3s04: Crystal structure of Escherichia coli type I signal peptidase in ... -

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Basic information

Entry
Database: PDB / ID: 3s04
TitleCrystal structure of Escherichia coli type I signal peptidase in complex with an Arylomycin Lipoglycopeptide Antibiotic
Components
  • Glyco-Arylomycin
  • Signal peptidase I
KeywordsHYDROLASE/ANTIBIOTIC / mostly-beta fold / Membrane bound / serine protease / Secreted preproteins / Cytoplasmic membrane / HYDROLASE-ANTIBIOTIC complex / signal peptidase / leader peptidase / signal peptide / leader peptide / serine-lysine dyad
Function / homology
Function and homology information


signal peptidase I / signal peptide processing / protein processing / peptidase activity / endopeptidase activity / serine-type endopeptidase activity / proteolysis / plasma membrane
Similarity search - Function
Signal Peptidase I; Chain: A, domain 2 / Signal Peptidase I; Chain: A, domain 2 - #10 / 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 Peptidase I; Chain: A, domain 2 / Signal Peptidase I; Chain: A, domain 2 - #10 / 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 / Umud Fragment, subunit A / Umud Fragment, subunit A / LexA/Signal peptidase-like superfamily / Beta Complex / Ribbon / Mainly Beta
Similarity search - Domain/homology
Arylomycin / 14-methylhexadec-9-enoic acid / alpha-L-rhamnopyranose / Signal peptidase I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Streptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsPaetzel, M. / Luo, C.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Synthesis and characterization of the arylomycin lipoglycopeptide antibiotics and the crystallographic analysis of their complex with signal peptidase.
Authors: Liu, J. / Luo, C. / Smith, P.A. / Chin, J.K. / Page, M.G. / Paetzel, M. / Romesberg, F.E.
History
DepositionMay 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2Nov 16, 2011Group: Database references
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Dec 6, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Remark 300THE BIOLOGICAL ASSEMBLY IS A HETERODIMER OF ONE SIGNAL PEPTIDASE I MOLECULE AND ONE ...THE BIOLOGICAL ASSEMBLY IS A HETERODIMER OF ONE SIGNAL PEPTIDASE I MOLECULE AND ONE GLYCOLIPOPEPTIDE INHIBITOR (GLYCO-ARYLOMYCIN) MOLECULE.

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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
I: Glyco-Arylomycin
J: Glyco-Arylomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3468
Polymers57,4814
Non-polymers8654
Water1,02757
1
A: Signal peptidase I
J: Glyco-Arylomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1734
Polymers28,7402
Non-polymers4332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-3 kcal/mol
Surface area10610 Å2
MethodPISA
2
B: Signal peptidase I
I: Glyco-Arylomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1734
Polymers28,7402
Non-polymers4332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-1 kcal/mol
Surface area11130 Å2
MethodPISA
3
A: Signal peptidase I
J: Glyco-Arylomycin
hetero molecules

B: Signal peptidase I
I: Glyco-Arylomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3468
Polymers57,4814
Non-polymers8654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x+1/2,-y+1/2,-z+1/41
Buried area4060 Å2
ΔGint-13 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.010, 72.010, 262.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 28079.814 Da / Num. of mol.: 2 / Fragment: Periplasmic domain, UNP residues 76-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2568, JW2552, lepB / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P00803, signal peptidase I
#2: Protein/peptide Glyco-Arylomycin


Type: Lipoglycopeptide / Class: Antibiotic / Mass: 660.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: BAL4850C IS A VARIANT OF THE LIPOGLYCO ARYLOMYCIN HERE BAL4850C IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE, THE LIPID (O2U) AND RHAMNOSE.
Source: (natural) Streptomyces sp. (bacteria) / References: Arylomycin
#3: Chemical ChemComp-02U / 14-methylhexadec-9-enoic acid


Type: Lipoglycopeptide / Class: Antibiotic / Mass: 268.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H32O2
Details: BAL4850C IS A VARIANT OF THE LIPOGLYCO ARYLOMYCIN HERE BAL4850C IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE, THE LIPID (O2U) AND RHAMNOSE.
References: Arylomycin
#4: Sugar ChemComp-RAM / alpha-L-rhamnopyranose / alpha-L-rhamnose / 6-deoxy-alpha-L-mannopyranose / L-rhamnose / rhamnose


Type: L-saccharide, alpha linking, Lipoglycopeptide / Class: Antibiotic / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
Details: BAL4850C IS A VARIANT OF THE LIPOGLYCO ARYLOMYCIN HERE BAL4850C IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE, THE LIPID (O2U) AND RHAMNOSE.
References: Arylomycin
IdentifierTypeProgram
LRhapaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-rhamnopyranoseCOMMON NAMEGMML 1.0
a-L-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE GLYCO-ARYLOMYCIN IS A CYCLIC LIPOHEXAPEPTIDE, A MEMBER OF THE ARYLOMYCIN FAMILY. ALL MEMBERS ...THE GLYCO-ARYLOMYCIN IS A CYCLIC LIPOHEXAPEPTIDE, A MEMBER OF THE ARYLOMYCIN FAMILY. ALL MEMBERS HAVE A FATTY ACID AT THE N-TERMINAL AND A CORE STRUCTURE OF TRIPEPTIDE MACROCYCLE FORMED BY A C-C BIARYL LINKAGE BETWEEN RESIDUES 5 AND 7. HERE, GLYCO-ARYLOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES), THE LIPID (02U) AND RHAMNOSE (RAM).
Sequence detailsRESIDUE 02V of CHAIN I AND J IS N-METHYL-DIHYDROXYPHENYLGLYCINE

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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: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 22% PEG 4000, 0.2M KCl, 0.025M n-dodecyl beta-D-maltoside (DDM), pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 19, 2005 / Details: mirrors
RadiationMonochromator: Osimic Confocal VariMax High Flux optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.44→32.2 Å / Num. all: 26783 / Num. obs: 26680 / % possible obs: 99.6 % / Observed criterion σ(I): 5 / Redundancy: 9.29 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 10.4
Reflection shellResolution: 2.44→2.53 Å / Redundancy: 10.89 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 5.1 / Num. unique all: 2605 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T7D

1t7d


Resolution: 2.44→32.2 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.921 / SU B: 18.315 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2647 1321 5 %RANDOM
Rwork0.24511 ---
obs0.24605 24852 97.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.028 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2--1.08 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 2.44→32.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3475 0 28 57 3560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223665
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0981.9895005
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2575438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9824.146164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69915564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3331520
X-RAY DIFFRACTIONr_chiral_restr0.0740.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222868
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3871.52174
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.72723530
X-RAY DIFFRACTIONr_scbond_it0.8931491
X-RAY DIFFRACTIONr_scangle_it1.6264.51468
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.44→2.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 87 -
Rwork0.329 1821 -
obs--98.6 %
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)
12.65272.7503-1.35774.9697-4.65658.5309-0.056-0.3269-0.4373-0.33790.08770.05891.3330.11-0.03170.63230.03010.03540.4350.02270.47113.5415-9.461454.8742
211.264-6.06026.372948.8787-20.881111.1474-0.1219-0.3753-0.3378-0.68660.45122.06980.8623-0.5953-0.32930.6369-0.17770.2090.6079-0.17660.6954-13.6604-8.511955.055
32.4828-1.09970.87814.8395-1.9714.44450.16910.2279-0.492-0.3118-0.11720.19390.8336-0.1443-0.05190.5216-0.1180.03380.4459-0.0280.4733-7.1403-5.188344.153
424.6455-0.816911.1661-12.1092-6.651819.8131-3.94131.01221.7771-0.99711.84050.05280.9973-6.43572.10081.3546-0.79080.03082.6076-0.52951.4884-24.2493-0.545442.866
512.8041-5.4608-4.88784.4977-1.846312.1052-0.23420.5498-0.2448-0.43720.09410.69910.2401-0.78620.14010.5860.0404-0.01740.49350.07160.4874-11.85619.829148.4792
69.3485-4.5172.207528.12084.30275.01780.60860.913-0.0362-1.38930.0008-0.86140.08760.528-0.60950.3626-0.11160.01470.4835-0.06020.488311.53386.738242.9166
727.2746.33290.441129.7594-2.37915.2205-0.2039-1.02790.14350.3470.5861-2.1976-0.36111.5877-0.38220.22330.00810.02190.70510.11370.494814.60898.055247.1738
89.7628-3.7317-10.66828.797820.12242.61820.86830.4251.5533-1.344-0.1113-2.4528-3.53192.4037-0.7570.4115-0.1842-0.00940.52340.27660.543716.392411.495441.3393
93.73081.484-1.11764.2625-0.44984.6533-0.15950.2402-0.0394-0.13410.17720.3540.4658-0.3864-0.01770.4468-0.05260.0030.43010.02430.4323-6.6315-0.373740.8803
105.87893.65562.1395.34463.7715.80750.0369-0.6245-0.34060.09680.0014-0.45010.49710.2729-0.03830.66030.05280.04450.48350.11220.47894.1438-7.612957.3098
117.51343.45922.610116.03423.34120.1625-0.2037-0.6370.20730.3684-0.2274-0.7007-1.8331-0.2290.43120.3942-0.02550.05140.46170.01280.5357-24.969139.523559.7078
121.8821.2858-0.58345.95923.50456.19540.0487-0.44770.23130.51420.0587-0.3299-0.29720.4778-0.10740.3947-0.0099-0.03290.30210.00250.4-22.09934.966757.8671
132.226-0.8097-1.44333.76541.8362.93180.2203-0.1650.4453-0.1045-0.0502-0.511-0.30860.1728-0.17010.4674-0.09390.03240.4420.03640.529-11.820334.696250.0384
143.6271-1.6161.41773.18181.39154.23620.11220.50040.0591-0.2280.0542-0.3167-0.25450.468-0.16640.5482-0.09590.11470.47860.08160.4288-15.476221.931746.1242
157.8231-2.053.5113.2964-2.15186.2928-0.02660.00010.0368-0.04130.02640.0759-0.0897-0.35090.00020.33850.00450.03450.2549-0.02520.3197-26.039623.698242.7517
169.66143.83192.56658.46524.81917.9319-0.24481.07660.4813-1.06380.6899-0.7002-1.07371.0213-0.44520.6495-0.15890.15550.56030.06620.651-4.303935.28641.7695
172.69211.3793-0.60162.38910.52113.19930.2667-0.21640.21040.1128-0.0395-0.1328-0.61680.0253-0.22720.4967-0.0324-0.00390.31820.07120.4612-17.788235.620151.8546
1872.064940.55692.116594.0571-43.455955.5805-1.30012.818-0.7286-3.4705-0.39970.0315-0.9708-0.69671.69981.50120.6116-0.38140.8177-0.22740.1605-36.460834.634846.3958
1914.3744-23.96517.061839.0048-25.3138.62560.7624-0.718-1.2915-1.29081.02762.3003-0.3081-2.7523-1.790.6317-0.19-0.1641.0840.20231.0107-38.718529.285254.9176
2011.593310.0962-9.37610.1914-9.97166.2351-0.1222-0.0751-1.1831-0.5158-0.6578-0.60820.58560.44070.781.48010.03490.12780.554-0.00340.2842-27.585626.441260.115
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A80 - 107
2X-RAY DIFFRACTION2A108 - 128
3X-RAY DIFFRACTION3A129 - 167
4X-RAY DIFFRACTION4A168 - 177
5X-RAY DIFFRACTION5A178 - 189
6X-RAY DIFFRACTION6A190 - 206
7X-RAY DIFFRACTION7A207 - 215
8X-RAY DIFFRACTION8A216 - 223
9X-RAY DIFFRACTION9A224 - 287
10X-RAY DIFFRACTION10A288 - 324
11X-RAY DIFFRACTION11B80 - 90
12X-RAY DIFFRACTION12B91 - 125
13X-RAY DIFFRACTION13B126 - 165
14X-RAY DIFFRACTION14B166 - 197
15X-RAY DIFFRACTION15B198 - 243
16X-RAY DIFFRACTION16B244 - 269
17X-RAY DIFFRACTION17B270 - 304
18X-RAY DIFFRACTION18B305 - 311
19X-RAY DIFFRACTION19B312 - 318
20X-RAY DIFFRACTION20B319 - 324

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