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- PDB-7thn: Crystal structure of PigI trapped with PigG using a proline adeno... -

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Basic information

Entry
Database: PDB / ID: 7thn
TitleCrystal structure of PigI trapped with PigG using a proline adenosine vinylsulfonamide inhibitor
Components
  • L-proline--[L-prolyl-carrier protein] ligase
  • Probable acyl carrier protein PigG
KeywordsLIGASE / nonribosomal peptide synthetase / NRPS / type II / biosynthesis / Ligase-Transport protein 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
ANL, C-terminal 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 / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily ...ANL, C-terminal 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 / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / Chem-I5M / L-proline--[L-prolyl-carrier protein] ligase / Probable acyl carrier protein PigG
Similarity search - Component
Biological speciesSerratia sp. ATCC 39006 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,06721
Polymers65,5132
Non-polymers1,55519
Water11,169620
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-17 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.670, 92.660, 66.770
Angle α, β, γ (deg.)90.000, 110.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules BE

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


Mass: 54823.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia sp. ATCC 39006 (bacteria) / Strain: ATCC 39006 / Gene: pigI / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q5W263, 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.: 1
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

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Non-polymers , 5 types, 639 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: N3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: 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.: 1 / Source method: obtained synthetically / Formula: C27H44N9O11PS2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.23
Details: 0.3 M MgCl2, 24.57% PEG 3350, and 0.1 M BIS-TRIS pH 6.23

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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: Aug 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.6→62.55 Å / Num. obs: 510902 / % possible obs: 99.92 % / Redundancy: 6.8 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1141 / Rpim(I) all: 0.04718 / Rrim(I) all: 0.1237 / Net I/σ(I): 12.66
Reflection shellResolution: 1.6→1.662 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.045 / Mean I/σ(I) obs: 1.62 / Num. unique obs: 7504 / CC1/2: 0.603 / CC star: 0.867 / Rpim(I) all: 0.4542 / Rrim(I) all: 1.142 / % possible all: 99.93

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6o6e

6o6e


Resolution: 1.6→62.55 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.763 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1874 3615 4.8 %RANDOM
Rwork0.1532 ---
obs0.1549 75380 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.1 Å2 / Biso mean: 17.858 Å2 / Biso min: 8.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.02 Å2
2--0.08 Å20 Å2
3----0.04 Å2
Refinement stepCycle: final / Resolution: 1.6→62.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4186 0 109 620 4915
Biso mean--25.12 31.27 -
Num. residues----556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134402
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174103
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.6465992
X-RAY DIFFRACTIONr_angle_other_deg1.5061.5779487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3755559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.71322.623183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30515673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5681521
X-RAY DIFFRACTIONr_chiral_restr0.1440.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024837
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02841
LS refinement shellResolution: 1.605→1.646 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 278 -
Rwork0.281 5271 -
all-5549 -
obs-7504 99.91 %

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