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- PDB-6b88: E. coli LepB in complex with GNE0775 ((4S,7S,10S)-10-((S)-4-amino... -

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Basic information

Entry
Database: PDB / ID: 6b88
TitleE. coli LepB in complex with GNE0775 ((4S,7S,10S)-10-((S)-4-amino-2-(2-(4-(tert-butyl)phenyl)-4-methylpyrimidine-5-carboxamido)-N-methylbutanamido)-16,26-bis(2-aminoethoxy)-N-(2-iminoethyl)-7-methyl-6,9-dioxo-5,8-diaza-1,2(1,3)-dibenzenacyclodecaphane-4-carboxamide)
ComponentsSignal peptidase I
KeywordsHYDROLASE/HYDROLASE inhibitor / Signal peptidase / SBDD / antibiotic / HYDROLASE / HYDROLASE-HYDROLASE inhibitor complex
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
Chem-CZD / Signal peptidase I
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.407 Å
AuthorsMurray, J.M. / Rouge, L.
CitationJournal: Nature / Year: 2018
Title: Optimized arylomycins are a new class of Gram-negative antibiotics.
Authors: Smith, P.A. / Koehler, M.F.T. / Girgis, H.S. / Yan, D. / Chen, Y. / Chen, Y. / Crawford, J.J. / Durk, M.R. / Higuchi, R.I. / Kang, J. / Murray, J. / Paraselli, P. / Park, S. / Phung, W. / ...Authors: Smith, P.A. / Koehler, M.F.T. / Girgis, H.S. / Yan, D. / Chen, Y. / Chen, Y. / Crawford, J.J. / Durk, M.R. / Higuchi, R.I. / Kang, J. / Murray, J. / Paraselli, P. / Park, S. / Phung, W. / Quinn, J.G. / Roberts, T.C. / Rouge, L. / Schwarz, J.B. / Skippington, E. / Wai, J. / Xu, M. / Yu, Z. / Zhang, H. / Tan, M.W. / Heise, C.E.
History
DepositionOct 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4955
Polymers55,4732
Non-polymers2,0223
Water1,78399
1
A: Signal peptidase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6282
Polymers27,7361
Non-polymers8921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Signal peptidase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8673
Polymers27,7361
Non-polymers1,1302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.980, 109.980, 116.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 77 through 114 or resid 116...
21(chain B and (resid 77 or (resid 78 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGILEILE(chain A and (resid 77 through 114 or resid 116...AA77 - 1141 - 38
12GLNGLNALAALA(chain A and (resid 77 through 114 or resid 116...AA116 - 20440 - 128
13THRTHRTHRTHR(chain A and (resid 77 through 114 or resid 116...AA205129
14ARGARGHISHIS(chain A and (resid 77 through 114 or resid 116...AA77 - 3231 - 247
15ARGARGHISHIS(chain A and (resid 77 through 114 or resid 116...AA77 - 3231 - 247
16ARGARGHISHIS(chain A and (resid 77 through 114 or resid 116...AA77 - 3231 - 247
17ARGARGHISHIS(chain A and (resid 77 through 114 or resid 116...AA77 - 3231 - 247
21ARGARGARGARG(chain B and (resid 77 or (resid 78 and (name...BB771
22SERSERSERSER(chain B and (resid 77 or (resid 78 and (name...BB782
23ARGARGHISHIS(chain B and (resid 77 or (resid 78 and (name...BB77 - 3231 - 247
24ARGARGHISHIS(chain B and (resid 77 or (resid 78 and (name...BB77 - 3231 - 247
25ARGARGHISHIS(chain B and (resid 77 or (resid 78 and (name...BB77 - 3231 - 247
26ARGARGHISHIS(chain B and (resid 77 or (resid 78 and (name...BB77 - 3231 - 247

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Components

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


Mass: 27736.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: lepB, b2568, JW2552 / Production host: Escherichia coli (E. coli) / References: UniProt: P00803, signal peptidase I
#2: Chemical ChemComp-CZD / (8S,11S,14S)-14-{[(2S)-4-amino-2-{[2-(4-tert-butylphenyl)-4-methylpyrimidine-5-carbonyl]amino}butanoyl](methyl)amino}-3,18-bis(2-aminoethoxy)-N-[(2Z)-2-iminoethyl]-11-methyl-10,13-dioxo-9,12-diazatricyclo[13.3.1.1~2,6~]icosa-1(19),2(20),3,5,15,17-hexaene-8-carboxamide


Mass: 892.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H61N11O7
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
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: 3.26 Å3/Da / Density % sol: 62.24 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 4.5 / Details: 30% PEG 300, 0.1 M Sodium Acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.372→79.969 Å / Num. obs: 27848 / % possible obs: 99.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 31.33 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.124 / Rrim(I) all: 0.235 / Net I/σ(I): 4.4 / Num. measured all: 96782
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.372-2.3793.21.3048122510.5230.841.5560.995.4
10.998-79.9693.50.08210292960.9880.0520.09811.598.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T7D

1t7d


Resolution: 2.407→54.99 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 26.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2646 1349 5.08 %
Rwork0.2384 25209 -
obs0.2397 26558 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.87 Å2 / Biso mean: 47.4306 Å2 / Biso min: 5.65 Å2
Refinement stepCycle: final / Resolution: 2.407→54.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3699 0 146 102 3947
Biso mean--34.71 32.44 -
Num. residues----479
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2224X-RAY DIFFRACTION5.177TORSIONAL
12B2224X-RAY DIFFRACTION5.177TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4071-2.49310.34421360.34062456259297
2.4931-2.5930.3431370.31082478261598
2.593-2.7110.35241200.30982522264299
2.711-2.85390.32771610.292519268099
2.8539-3.03270.26521460.262325022648100
3.0327-3.26680.31161260.250525272653100
3.2668-3.59550.27921340.207225522686100
3.5955-4.11560.20331510.20312490264199
4.1156-5.18470.2142990.18632582268199
5.1847-55.00430.22221390.23742581272099
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)
14.0353-0.5686-0.2813.4655-0.2685.0769-0.0195-0.07130.03920.29360.13990.2872-0.0496-0.22280.02430.2427-0.0011-0.0190.14410.00320.17785.063144.77697.6418
25.6846-1.4125-0.52062.98710.29124.8628-0.4285-0.6560.32290.0361-0.02721.5869-0.0875-1.6374-0.00390.51080.08790.11480.816-0.09540.7129-6.952338.669118.7402
34.2899-0.88220.26673.59380.38374.84810.3743-0.7743-0.62830.6349-0.607-0.18351.23920.0516-0.11210.47940.18120.030.3062-0.0370.142814.587130.203815.5183
42.9271-0.64640.1063.4089-0.38114.49710.26980.87760.00170.41940.1907-1.2112-0.12881.3694-0.12130.38720.02920.00840.89-0.18930.459925.885435.7028-1.7453
53.82750.5842-0.13454.0495-0.31264.3233-0.50992.14730.34020.1643-0.229-2.292-0.35411.9021-0.06690.3644-0.0060.18291.038-0.2816-0.001424.530238.1251-5.5013
62.8402-0.75510.21832.53040.02134.5175-0.2279-0.2292-0.38420.380.2522-0.33160.82010.483-0.12820.51230.2117-0.06890.3577-0.00620.281320.600629.889714.4384
73.3629-1.48761.26032.4958-0.26234.2026-0.02560.2069-0.01440.11050.0973-0.10480.40470.3123-0.02260.19950.01270.01620.1939-0.05340.1612.291940.71236.8773
81.9902-0.54490.89223.23020.95644.6541-0.02690.30410.152-0.36580.0757-0.37720.15320.3816-0.05040.2851-0.070.02640.25120.01530.1758-3.791340.0486-19.1429
93.40260.84220.19273.65680.08885.59720.0708-0.1126-0.6152-0.577-0.06720.61070.9516-0.1913-0.02970.6638-0.202-0.16060.40080.07020.3123-17.022525.3831-12.7194
103.3221-0.6356-0.83983.99370.86374.8728-0.0761-0.8322-0.22130.744-0.14771.00880.7296-1.13980.02240.4041-0.2912-0.04550.7032-0.05080.3893-22.541835.4589-0.9993
111.85950.5169-0.27032.38050.59144.7193-0.12770.0824-0.2289-0.37090.01850.44220.7645-0.5776-0.01060.5074-0.2023-0.0540.3039-0.01070.3007-16.911328.7082-19.2731
121.51320.9020.89992.07570.91374.742-0.1584-0.0916-0.06980.046-0.0118-0.03020.2616-0.1501-0.03160.1953-0.07860.00480.24060.03240.1901-8.227241.5708-11.9175
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 77 through 110 )A77 - 110
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 129 )A111 - 129
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 181 )A130 - 181
4X-RAY DIFFRACTION4chain 'A' and (resid 182 through 203 )A182 - 203
5X-RAY DIFFRACTION5chain 'A' and (resid 204 through 230 )A204 - 230
6X-RAY DIFFRACTION6chain 'A' and (resid 231 through 268 )A231 - 268
7X-RAY DIFFRACTION7chain 'A' and (resid 269 through 323 )A269 - 323
8X-RAY DIFFRACTION8chain 'B' and (resid 77 through 158 )B77 - 158
9X-RAY DIFFRACTION9chain 'B' and (resid 159 through 201 )B159 - 201
10X-RAY DIFFRACTION10chain 'B' and (resid 202 through 230 )B202 - 230
11X-RAY DIFFRACTION11chain 'B' and (resid 231 through 280 )B231 - 280
12X-RAY DIFFRACTION12chain 'B' and (resid 281 through 323 )B281 - 323

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