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- PDB-2dnw: Solution structure of RSGI RUH-059, an ACP domain of acyl carrier... -

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Basic information

Entry
Database: PDB / ID: 2dnw
TitleSolution structure of RSGI RUH-059, an ACP domain of acyl carrier protein, mitochondrial [Precursor] from human cDNA
ComponentsAcyl carrier protein
KeywordsTRANSPORT PROTEIN / acyl carrier protein / ACP / fatty acid biosynthesis / mitochondria / NADH:ubiquinone oxidereductase / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Respiratory electron transport / protein lipoylation / Glyoxylate metabolism and glycine degradation / acyl binding / acyl carrier activity / mitochondrial respiratory chain complex I assembly / mitochondrial respiratory chain complex I / mitochondrial electron transport, NADH to ubiquinone ...Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / Respiratory electron transport / protein lipoylation / Glyoxylate metabolism and glycine degradation / acyl binding / acyl carrier activity / mitochondrial respiratory chain complex I assembly / mitochondrial respiratory chain complex I / mitochondrial electron transport, NADH to ubiquinone / mitochondrial membrane / fatty acid binding / fatty acid biosynthetic process / mitochondrial inner membrane / mitochondrial matrix / calcium ion binding / mitochondrion / nucleoplasm
Similarity search - Function
ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Acyl carrier protein (ACP) / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Acyl carrier protein, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsAbe, T. / Hirota, H. / Kurosaki, C. / Yoshida, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of RSGI RUH-059, an ACP domain of acyl carrier protein, mitochondrial [Precursor] from human cDNA
Authors: Abe, T. / Hirota, H. / Kurosaki, C. / Yoshida, M. / Yokoyama, S.
History
DepositionApr 26, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl carrier protein


Theoretical massNumber of molelcules
Total (without water)10,9681
Polymers10,9681
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, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy, target function

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Components

#1: Protein Acyl carrier protein / / ACP / NADH-ubiquinone oxidoreductase 9.6 kDa subunit / CI-SDAP


Mass: 10968.360 Da / Num. of mol.: 1 / Fragment: acyl carrier protein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: NDUFAB1 / Plasmid: P050704-29 / Production host: Cell free synthesis / References: UniProt: O14561

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 0.91mM RSGI RUH-059 U-15N, 13C; 20mM d-Tris-HCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: JEOL ECA / Manufacturer: JEOL / Model: ECA / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Delta NMR4.3.2JEOLcollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.932Kobayashi, N.data analysis
CYANA1.0.8Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy, target function
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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