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- PDB-7thq: Crystal structure of PltF trapped with PigG using a proline adeno... -

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Basic information

Entry
Database: PDB / ID: 7thq
TitleCrystal structure of PltF trapped with PigG using a proline adenosine vinylsulfonamide inhibitor
Components
  • L-proline--[L-prolyl-carrier protein] ligase
  • Probable acyl carrier protein PigG
KeywordsLIGASE/LIGASE INHIBITOR / nonribosomal peptide synthetase / NRPS / type II / biosynthesis / Ligase-Transport protein complex / LIGASE / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


L-proline-[L-prolyl-carrier protein] ligase / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / ligase activity / phosphopantetheine binding / antibiotic biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
AMP-binding / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily ...AMP-binding / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
AZIDE ION / Chem-I5M / L-proline--[L-prolyl-carrier protein] ligase / Probable acyl carrier protein PigG
Similarity search - Component
Biological speciesPseudomonas protegens Pf-5 (bacteria)
Serratia sp. ATCC 39006 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsCorpuz, J.C. / Podust, L.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008326 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1F31GM13761601A1 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM095970 United States
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Essential Role of Loop Dynamics in Type II NRPS Biomolecular Recognition.
Authors: Corpuz, J.C. / Patel, A. / Davis, T.D. / Podust, L.M. / McCammon, J.A. / Burkart, M.D.
History
DepositionJan 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: L-proline--[L-prolyl-carrier protein] ligase
E: Probable acyl carrier protein PigG
A: L-proline--[L-prolyl-carrier protein] ligase
C: Probable acyl carrier protein PigG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,95712
Polymers134,1744
Non-polymers1,7848
Water88349
1
B: L-proline--[L-prolyl-carrier protein] ligase
E: Probable acyl carrier protein PigG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9796
Polymers67,0872
Non-polymers8924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-13 kcal/mol
Surface area23160 Å2
MethodPISA
2
A: L-proline--[L-prolyl-carrier protein] ligase
C: Probable acyl carrier protein PigG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9796
Polymers67,0872
Non-polymers8924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-11 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.730, 132.680, 140.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 119 or (resid 120...
21(chain B and (resid 1 through 16 or (resid 17...
12(chain C and ((resid 1 through 2 and (name N...
22(chain E and (resid 1 through 4 or (resid 5...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETALAALA(chain A and (resid 1 through 119 or (resid 120...AC1 - 1191 - 119
121GLNGLNGLNGLN(chain A and (resid 1 through 119 or (resid 120...AC120120
131METMETLEULEU(chain A and (resid 1 through 119 or (resid 120...AC1 - 5041 - 504
141METMETLEULEU(chain A and (resid 1 through 119 or (resid 120...AC1 - 5041 - 504
151METMETLEULEU(chain A and (resid 1 through 119 or (resid 120...AC1 - 5041 - 504
161METMETLEULEU(chain A and (resid 1 through 119 or (resid 120...AC1 - 5041 - 504
211METMETPROPRO(chain B and (resid 1 through 16 or (resid 17...BA1 - 161 - 16
221ARGARGARGARG(chain B and (resid 1 through 16 or (resid 17...BA1717
231METMETGLUGLU(chain B and (resid 1 through 16 or (resid 17...BA1 - 5051 - 505
241METMETGLUGLU(chain B and (resid 1 through 16 or (resid 17...BA1 - 5051 - 505
251METMETGLUGLU(chain B and (resid 1 through 16 or (resid 17...BA1 - 5051 - 505
261METMETGLUGLU(chain B and (resid 1 through 16 or (resid 17...BA1 - 5051 - 505
271METMETGLUGLU(chain B and (resid 1 through 16 or (resid 17...BA1 - 5051 - 505
281METMETGLUGLU(chain B and (resid 1 through 16 or (resid 17...BA1 - 5051 - 505
112METMETLEULEU(chain C and ((resid 1 through 2 and (name N...CD1 - 21 - 2
122METMETLEULEU(chain C and ((resid 1 through 2 and (name N...CD1 - 771 - 77
132METMETLEULEU(chain C and ((resid 1 through 2 and (name N...CD1 - 771 - 77
142METMETLEULEU(chain C and ((resid 1 through 2 and (name N...CD1 - 771 - 77
152METMETLEULEU(chain C and ((resid 1 through 2 and (name N...CD1 - 771 - 77
212METMETSERSER(chain E and (resid 1 through 4 or (resid 5...EB1 - 41 - 4
222LYSLYSLYSLYS(chain E and (resid 1 through 4 or (resid 5...EB55
232METMETALAALA(chain E and (resid 1 through 4 or (resid 5...EB1 - 791 - 79
242METMETALAALA(chain E and (resid 1 through 4 or (resid 5...EB1 - 791 - 79
252METMETALAALA(chain E and (resid 1 through 4 or (resid 5...EB1 - 791 - 79

NCS ensembles :
ID
1
2

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Components

#1: Protein L-proline--[L-prolyl-carrier protein] ligase / L-prolyl-AMP ligase


Mass: 56397.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas protegens Pf-5 (bacteria) / Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: pltF, PFL_2792 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q4KCY5, L-proline-[L-prolyl-carrier protein] ligase
#2: Protein Probable acyl carrier protein PigG / Peptidyl carrier protein / PCP


Mass: 10689.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia sp. ATCC 39006 (bacteria) / Strain: ATCC 39006 / Gene: pigG / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5W265
#3: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: N3
#4: Chemical ChemComp-I5M / 5'-deoxy-5'-({(2S)-2-({2-[(N-{(2R)-4-[(dioxo-lambda~5~-phosphanyl)oxy]-2-hydroxy-3,3-dimethylbutanoyl}-beta-alanyl)amino]ethyl}sulfanyl)-2-[(2S)-pyrrolidin-2-yl]ethanesulfonyl}amino)adenosine


Mass: 765.796 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H44N9O11PS2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 35% PEG 3350, 0.50 M NaCl, 0.1 M BTP pH 7.50, and 0.01 M sodium citrate tribasic

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.46→96.61 Å / Num. obs: 45189 / % possible obs: 99.09 % / Redundancy: 12.8 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1532 / Rpim(I) all: 0.04389 / Rrim(I) all: 0.1595 / Net I/σ(I): 13.99
Reflection shellResolution: 2.46→2.548 Å / Redundancy: 10.4 % / Rmerge(I) obs: 2.666 / Num. unique obs: 4110 / CC1/2: 0.286 / CC star: 0.667 / Rpim(I) all: 0.8246 / Rrim(I) all: 2.798 / % possible all: 91.27

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6o6e

6o6e


Resolution: 2.46→96.61 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 2303 5.12 %
Rwork0.2061 42634 -
obs0.2086 44937 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.12 Å2 / Biso mean: 68.5203 Å2 / Biso min: 39.93 Å2
Refinement stepCycle: final / Resolution: 2.46→96.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8443 0 118 49 8610
Biso mean--65.1 72.35 -
Num. residues----1161
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3068X-RAY DIFFRACTION9.734TORSIONAL
12B3068X-RAY DIFFRACTION9.734TORSIONAL
21C456X-RAY DIFFRACTION9.734TORSIONAL
22E456X-RAY DIFFRACTION9.734TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.46-2.510.37671020.35341915201771
2.51-2.570.37561270.326326612788100
2.57-2.630.37041400.312227072847100
2.63-2.70.33621380.308926542792100
2.7-2.780.38681440.299426692813100
2.78-2.870.34961550.28226922847100
2.87-2.980.32321400.268926822822100
2.98-3.090.30871260.248427052831100
3.09-3.240.2861310.234127052836100
3.24-3.410.2641420.228127032845100
3.41-3.620.25151750.202626972872100
3.62-3.90.24391810.187126772858100
3.9-4.290.23661680.167226972865100
4.29-4.910.20391400.158727622902100
4.91-6.190.24541370.191427872924100
6.19-96.610.21291570.18329213078100
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)
11.07560.30440.18152.1155-0.12641.0269-0.03310.07390.0341-0.1780.0517-0.0141-0.1417-0.0137-0.01110.36440.0271-0.00420.4599-0.10230.3482-29.183-12.93311.12
23.36210.73250.78735.8541-0.07440.1879-0.26840.1682-0.092-0.84770.59580.51430.2005-0.836-0.30450.8608-0.1871-0.13161.05840.05050.504-40.872-9.957-14.695
31.9325-0.06330.19532.60860.45072.22480.01820.3367-0.2082-0.2674-0.0365-0.27570.1630.24910.01420.34850.00870.04750.4712-0.00360.4198-20.09826.8125.758
46.74371.36510.73123.9346-0.46631.52020.0590.38460.3318-0.0142-0.2854-0.09620.00930.02790.28590.63330.04910.15691.16880.02861.05727.51125.08320.648
50.0610.3633-0.09572.04890.3840.1982-0.04770.03320.04120.2820.2348-0.05980.06730.1554-0.19070.31080.06770.01780.57970.00420.3122-28.161-2.63821.472
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 1:505 )B1 - 505
2X-RAY DIFFRACTION2( CHAIN E AND RESID 1:79 )E1 - 79
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1:504 )A1 - 504
4X-RAY DIFFRACTION4( CHAIN C AND RESID 2:77 )C2 - 77
5X-RAY DIFFRACTION5( CHAIN A AND RESID 801:819 ) OR ( CHAIN B AND RESID 801:823 ) OR ( CHAIN C AND RESID 1002:1002 ) OR ( CHAIN E AND RESID 1101:1101 )A801 - 819
6X-RAY DIFFRACTION5( CHAIN A AND RESID 801:819 ) OR ( CHAIN B AND RESID 801:823 ) OR ( CHAIN C AND RESID 1002:1002 ) OR ( CHAIN E AND RESID 1101:1101 )B801 - 823
7X-RAY DIFFRACTION5( CHAIN A AND RESID 801:819 ) OR ( CHAIN B AND RESID 801:823 ) OR ( CHAIN C AND RESID 1002:1002 ) OR ( CHAIN E AND RESID 1101:1101 )C1002
8X-RAY DIFFRACTION5( CHAIN A AND RESID 801:819 ) OR ( CHAIN B AND RESID 801:823 ) OR ( CHAIN C AND RESID 1002:1002 ) OR ( CHAIN E AND RESID 1101:1101 )E1101

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