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- PDB-1f03: SOLUTION STRUCTURE OF OXIDIZED BOVINE MICROSOMAL CYTOCHROME B5 MU... -

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Entry
Database: PDB / ID: 1f03
TitleSOLUTION STRUCTURE OF OXIDIZED BOVINE MICROSOMAL CYTOCHROME B5 MUTANT (E44A, E48A, E56A, D60A) AND ITS INTERACTION WITH CYTOCHROME C
ComponentsCYTOCHROME B5
KeywordsELECTRON TRANSPORT / CYTOCHROME B5 / PROTEIN RECOGNITION / SOLUTION STRUCTURE / PARAMAGNETIC NMR
Function / homology
Function and homology information


Vitamin C (ascorbate) metabolism / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / mitochondrial outer membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / heme binding / metal ion binding
Similarity search - Function
: / Flavocytochrome B2; Chain A, domain 1 / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain ...: / Flavocytochrome B2; Chain A, domain 1 / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain / Roll / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome b5
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / TORSION ANGLE MOLECULAR
Model type detailsminimized average
AuthorsWu, Y.B. / Lu, J. / Qian, C.M. / Tang, W.X. / Li, E.C. / Wang, J.F. / Wang, Y.H. / Wang, W.H. / Lu, J.X. / Xie, Y. / Huang, Z.X.
CitationJournal: Eur.J.Biochem. / Year: 2001
Title: Solution structure of cytochrome b(5) mutant (E44/48/56A/D60A) and its interaction with cytochrome c.
Authors: Wu, Y. / Wang, Y. / Qian, C. / Lu, J. / Li, E. / Wang, W. / Lu, J. / Xie, Y. / Wang, J. / Zhu, D. / Huang, Z. / Tang, W.
History
DepositionMay 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME B5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8742
Polymers9,2571
Non-polymers6161
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 35target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein CYTOCHROME B5


Mass: 9257.262 Da / Num. of mol.: 1 / Mutation: E44A, E48A, E56A, D60A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PUC 19 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P00171
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1222D NOESY
131DQF-COSY
142DQF-COSY
151TOCSY
162TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
16 mM cytochrome b5 mutant 1H10 mM phosphate buffer, 90% H2O, 10% D2O
26 mM cytochrome b5 mutant 1H10 mM phosphate buffer, D2O
Sample conditionsIonic strength: 10 mM / pH: 7 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA5Gntert, Mumenthaler, Wthrichstructure solution
PSEUDODYANABanci, Bertini, Cremonini, Gori Savellini, Luchinat, Wthrich, Gntertstructure solution
Amber5Pearlman, Case, Caldwell, Ross, Cheatham, Ferguson, Seibel, Singh, Weiner, Kollmanrefinement
PSEUDOREMBanci, Bertini, Gori Savellini, Romagnoli, Turano, Cremonini, Luchinat, Garyrefinement
RefinementMethod: TORSION ANGLE MOLECULAR / Software ordinal: 1
Details: DYNAMICS SIMULATED ANNEALING, RESTRAINED ENERGY MINIMIZATION; PSEUDOCONTACT SHIFTS WERE USED IN THE CALCULATION AND IN THE MINIMIZATION AS FURTHER NON-CLASSICAL CONSTRAINTS
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 35 / Conformers submitted total number: 1

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