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- PDB-2l6p: NMR solution structure of the protein NP_253742.1 -

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Basic information

Entry
Database: PDB / ID: 2l6p
TitleNMR solution structure of the protein NP_253742.1
ComponentsPhaC1, phaC2 and phaD genes
KeywordsStructure Genomics / unknown function / DUF971 / Structural Genomics / PSI-Biology / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homologyGamma-butyrobetaine hydroxylase-like, N-terminal / GBBH-like, N-terminal domain superfamily / Gamma-butyrobetaine hydroxylase-like, N-terminal / isomerase activity / metal ion binding / 1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 10
AuthorsMohanty, B. / Serrano, P. / Geralt, M. / Horst, R. / Wuthrich, K. / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: NMR solution structure of the protein NP_253742.1
Authors: Mohanty, B. / Serrano, P. / Geralt, M. / Horst, R. / Wuthrich, K.
History
DepositionNov 23, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 3, 2011Group: Structure summary
Revision 1.3Feb 22, 2012Group: Structure summary
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PhaC1, phaC2 and phaD genes


Theoretical massNumber of molelcules
Total (without water)13,7261
Polymers13,7261
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 / 80CYANA target function
RepresentativeModel #1closest to the average

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Components

#1: Protein PhaC1, phaC2 and phaD genes / uncharacterized protein NP_253742.1


Mass: 13726.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA5055 / Plasmid: pSpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q51512

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1314D APSY-HACANH
1415D APSY-(HA)CA(CO)NH
1515D APSY-CBCA(CO)NH
16115N resolved [1H,1H]-NOESY
17113Cali resolved [1H,1H]-NOESY
18113Caro resolved [1H,1H]-NOESY
19115 N {1H} - NOE

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Sample preparation

DetailsContents: 50 mM sodium chloride, 20 mM sodium phosphate, 4.5 mM sodium azide, 1.2 mM [U-98% 13C; U-98% 15N] protein-NP_253742.1-4, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium chloride-11
20 mMsodium phosphate-21
4.5 mMsodium azide-31
1.2 mMprotein-NP_253742.1-4[U-98% 13C; U-98% 15N]1
Sample conditionsIonic strength: 0.113 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
UNIO2.0.1Herrmann and Wuthrichstructure solution
OPALLuginbuhl, Guntert, Billeter and Wuthrichenergy refinement
CARAKeller and Wuthrichchemical shift assignment
TopSpin1.3Bruker Biospinacquisition
TopSpin1.3Bruker Biospinprocessing
TopSpin1.3Bruker Biospindata analysis
UNIO2.0.1Herrmann and Wuthrichrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: OPALp
NMR constraintsNOE constraints total: 2113 / NOE intraresidue total count: 526 / NOE long range total count: 569 / NOE medium range total count: 427 / NOE sequential total count: 591 / Protein chi angle constraints total count: 107 / Protein phi angle constraints total count: 117 / Protein psi angle constraints total count: 123
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: CYANA target function / Conformers calculated total number: 80 / Conformers submitted total number: 20

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