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- PDB-1axx: THE SOLUTION STRUCTURE OF OXIDIZED RAT MICROSOMAL CYTOCHROME B5, ... -

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Basic information

Entry
Database: PDB / ID: 1axx
TitleTHE SOLUTION STRUCTURE OF OXIDIZED RAT MICROSOMAL CYTOCHROME B5, NMR, 19 STRUCTURES
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 / response to cadmium ion / mitochondrial outer membrane / electron transfer activity / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / endoplasmic reticulum ...Vitamin C (ascorbate) metabolism / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / response to cadmium ion / mitochondrial outer membrane / electron transfer activity / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / endoplasmic reticulum / membrane / 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 speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / TORSION ANGLE MOLECULAR DYNAMICS SIMULATED ANNEALING, RESTRAINED ENERGY MINIMIZATION; PSEUDOCONTACT SHIFTS WERE USED IN THE CALCULATION, IN THE MINIMIZATION AS FURTHER NON-CLASSICAL CONSTRAINTS
AuthorsArnesano, F. / Banci, L. / Bertini, I. / Felli, I.C.
CitationJournal: Biochemistry / Year: 1998
Title: The solution structure of oxidized rat microsomal cytochrome b5.
Authors: Arnesano, F. / Banci, L. / Bertini, I. / Felli, I.C.
History
DepositionOct 22, 1997Processing site: BNL
Revision 1.0Mar 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 23, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_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)11,4302
Polymers10,8141
Non-polymers6161
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 40FAMILY OF MINIMIZED STRUCTURES
Representative

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Components

#1: Protein CYTOCHROME B5


Mass: 10813.908 Da / Num. of mol.: 1 / Fragment: SOLUBLE DOMAIN
Source method: isolated from a genetically manipulated source
Details: FROM RAT MICROSOMAL MEMBRANE / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Organelle: MICROSOME / Plasmid: PUC 13 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): NM522 / References: UniProt: P00173
#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
111NOESY
121TOCSY
1311D NOE

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Sample preparation

Sample conditionsIonic strength: 1 mM PHOSPHATE / pH: 7 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AVANCE 800 MHZ / Manufacturer: Bruker / Model: AVANCE 800 MHZ / Field strength: 800 MHz

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Processing

Software
NameClassification
DYANAmodel building
AMBERrefinement
DYANArefinement
NMR software
NameDeveloperClassification
AmberPEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
DYANAstructure solution
PSEUDYANAstructure solution
Amberstructure solution
RefinementMethod: TORSION ANGLE MOLECULAR DYNAMICS SIMULATED ANNEALING, RESTRAINED ENERGY MINIMIZATION; PSEUDOCONTACT SHIFTS WERE USED IN THE CALCULATION, IN THE MINIMIZATION AS FURTHER NON-CLASSICAL CONSTRAINTS
Software ordinal: 1
Details: PSEUDOREM (BANCI,BERTINI, GORI SAVELLINI,ROMAGNOLI,TURANO,CREMONINI,LUCHINAT, GRAY) ALSO WAS USED.
NMR ensembleConformer selection criteria: FAMILY OF MINIMIZED STRUCTURES
Conformers calculated total number: 40 / Conformers submitted total number: 19

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