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- PDB-5jdx: PigG holo -

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Basic information

Entry
Database: PDB / ID: 5jdx
TitlePigG holo
ComponentsPutative peptidyl carrier protein
KeywordsTRANSPORT PROTEIN / peptidyl carrier protein / prodigiosin / pyrrole
Function / homologyantibiotic biosynthetic process / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / 4'-PHOSPHOPANTETHEINE / Probable acyl carrier protein PigG
Function and homology information
Biological speciesSerratia sp. (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsJaremko, M.J. / Lee, D.J. / Burkart, M.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA009523 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095970 United States
CitationJournal: To Be Published
Title: PigG holo
Authors: Jaremko, M.J. / Lee, D.J. / Burkart, M.D.
History
DepositionApr 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative peptidyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1452
Polymers9,7871
Non-polymers3581
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20target function
RepresentativeModel #1target function

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Components

#1: Protein Putative peptidyl carrier protein / PigG holo


Mass: 9787.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia sp. (bacteria) / Gene: pigG / Production host: Escherichia coli (E. coli) / References: UniProt: Q5W265
#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H23N2O7PS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D HNCO
141isotropic13D CBCA(CO)NH
151isotropic13D 1H-15N NOESY
161isotropic13D 1H-13C NOESY aliphatic
171isotropic13D 1H-13C NOESY aromatic
181isotropic12D 1H-13C HSQC
191isotropic13D (H)CCH-TOCSY

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Sample preparation

DetailsType: solution
Contents: 1.5 mM [U-13C; U-15N] PigG, 50 mM KPi, 5 mM TCEP, .1 % sodium azide, 90% H2O/10% D2O
Label: 15N-13C_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMPigG[U-13C; U-15N]1
50 mMKPinatural abundance1
5 mMTCEPnatural abundance1
.1 %sodium azidenatural abundance1
Sample conditionsIonic strength: 50 mM / Label: Conditions_1 / pH: 7.4 / Pressure: 1 atm / Temperature: 25 C

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NMR measurement

NMR spectrometerType: Varian vs800 / Manufacturer: Varian / Model: vs800 / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 20 / Conformers submitted total number: 20

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