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- PDB-2n6y: Solution structure of holo ArCP from yersiniabactin synthetase -

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Basic information

Entry
Database: PDB / ID: 2n6y
TitleSolution structure of holo ArCP from yersiniabactin synthetase
ComponentsHMWP2 nonribosomal peptide synthetase
KeywordsLIGASE / Carrier Protein / Holo / Nonribosomal Peptide Synthetase / Yersiniabactin
Function / homology
Function and homology information


toxin biosynthetic process / amide biosynthetic process / phosphopantetheine binding / catalytic activity
Similarity search - Function
Methyltransferase type 12 / Methyltransferase domain / ACP-like / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily ...Methyltransferase type 12 / Methyltransferase domain / ACP-like / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Yersiniabactin biosynthetic protein / Yersiniabactin biosynthetic protein
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsGoodrich, A.C. / Harden, B.J. / Frueh, D.P.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Solution Structure of a Nonribosomal Peptide Synthetase Carrier Protein Loaded with Its Substrate Reveals Transient, Well-Defined Contacts.
Authors: Goodrich, A.C. / Harden, B.J. / Frueh, D.P.
History
DepositionAug 31, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Oct 7, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HMWP2 nonribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)10,1111
Polymers10,1111
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein HMWP2 nonribosomal peptide synthetase / Yersiniabactin biosynthetic protein


Mass: 10111.398 Da / Num. of mol.: 1 / Fragment: UNP residues 14-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: irp2, y2399, YPO1911 / Plasmid: pET-DUET-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CI41, UniProt: A0A3N4B635*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D HNCO
1323D HNCA
1423D HN(CO)CA
1523D H(CCO)NH
1623D HN(CA)CB
1713D 1H-15N NOESY
1822D 1H-13C HSQC
1923D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3-0.5 mM [U-99% 15N] Holo-ArCP, 50 mM ACES, 0.5 mM TCEP, 150 mM sodium chloride, 1 mM magnesium chloride, 0.1 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
20.3-0.5 mM [U-99% 13C; U-99% 15N] Holo-ArCP, 50 mM ACES, 0.5 mM TCEP, 150 mM sodium chloride, 1 mM magnesium chloride, 0.1 mM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMHolo-ArCP-1[U-99% 15N]0.3-0.51
50 mMACES-21
0.5 mMTCEP-31
150 mMsodium chloride-41
1 mMmagnesium chloride-51
0.1 mMDSS-61
mMHolo-ArCP-7[U-99% 13C; U-99% 15N]0.3-0.52
50 mMACES-82
0.5 mMTCEP-92
150 mMsodium chloride-102
1 mMmagnesium chloride-112
0.1 mMDSS-122
Sample conditionspH: 6.80 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichpeak picking
CARAKeller and Wuthrichdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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