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- PDB-1yyj: The NMR solution structure of a redesigned apocytochrome b562:Rd-... -

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Basic information

Entry
Database: PDB / ID: 1yyj
TitleThe NMR solution structure of a redesigned apocytochrome b562:Rd-apocyt b562
Componentsredesigned apocytochrome B562
KeywordsDE NOVO PROTEIN / four Helix protein / Structural Genomics / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
Function / homologyCytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics
AuthorsFeng, H. / Takei, J. / Lipsitz, R. / Tjandra, N. / Bai, Y. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Biochemistry / Year: 2003
Title: Specific non-native hydrophobic interactions in a hidden folding intermediate: implications for protein folding
Authors: Feng, H. / Takei, J. / Lipsitz, R. / Tjandra, N. / Bai, Y.
History
DepositionFeb 25, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Sep 27, 2023Group: Data collection / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond / pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: redesigned apocytochrome B562


Theoretical massNumber of molelcules
Total (without water)11,7291
Polymers11,7291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100
RepresentativeModel #1

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Components

#1: Protein redesigned apocytochrome B562


Mass: 11729.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D HSQC
1213D 13C-separated NOESY
1313D 15N-separated NOESY
141HNHA
1513D HN(CA)CB, 3D CBCA(CO)NH
1613D HBHA(CO)NH
NMR detailsText: Residual dipolar coupling, 2D NOESY, 3D HNCA, etc.

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Sample preparation

DetailsContents: 1.5mM Rd apocytochrome B562, 15N and/or 13C uniformly labeled
Solvent system: 50mM Sodium acetate, pH 4.84, 92.5% H2O, 7.5% D2O
Sample conditionspH: 4.84 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX7502

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Processing

NMR software
NameVersionClassification
X-PLORNIH-2.9structure solution
NMRPipeprocessing
X-PLORNIH-2.9refinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics
Software ordinal: 1
NMR ensembleConformers calculated total number: 100 / Conformers submitted total number: 10

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