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- PDB-1yzc: The solution structure of a redesigned apocytochrome B562 (Rd-apo... -

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Basic information

Entry
Database: PDB / ID: 1yzc
TitleThe solution structure of a redesigned apocytochrome B562 (Rd-apocyt b562) with the N- and a part of the C-terminal helices unfolded
Componentsedesigned apo-cytochrome b562
KeywordsELECTRON TRANSPORT / Folding intermediates / native-state hydrogen exchange / protein engineering / protein structure / Structural Genomics / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
Function / homology
Function and homology information


electron transfer activity / periplasmic space / iron ion binding / heme binding
Similarity search - Function
Cytochrome c/b562 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Soluble cytochrome b562
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics matrix relaxation torsion angle dynamics
AuthorsFeng, H. / Zhou, Z. / Bai, Y. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: A protein folding pathway with multiple folding intermediates at atomic resolution
Authors: Feng, H. / Zhou, Z. / Bai, Y.
History
DepositionFeb 28, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2006Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: edesigned apo-cytochrome b562


Theoretical massNumber of molelcules
Total (without water)11,1791
Polymers11,1791
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)10 / 100
RepresentativeModel #1

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Components

#1: Protein edesigned apo-cytochrome b562


Mass: 11179.256 Da / Num. of mol.: 1 / Mutation: W7D, L10G, L14G, V16G, I17G, I98G, Y101G, Y105G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: ET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS cells / References: UniProt: Q0SXH8*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D HSQC
1213D 15N-separated NOESY
1313D 13C-separated NOESY
141HNHA
1513D HN(CA)CB, 3D CBCA(CO)NH
1613D HAHBCONH, 3D HNCO, 2D NOESY
1722D NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
150mM sodium acetate; 92.5% H2O, 7.5% D2O92.5% H2O, 7.5% D2O
250mM sodium acetate; 99% D2O99% D2O
Sample conditionspH: 4.84 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe5.0.4Delaglio, F.processing
X-PLORNIH-2.9structure solution
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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