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- PDB-1mny: Dimethyl propionate ester heme-containing cytochrome b5 -

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Basic information

Entry
Database: PDB / ID: 1mny
TitleDimethyl propionate ester heme-containing cytochrome b5
Componentscytochrome b5
KeywordsELECTRON TRANSPORT / heme / iron / microsomal membrane
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 / endoplasmic reticulum membrane / heme binding / 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 / endoplasmic reticulum membrane / heme binding / 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
DIMETHYL PROPIONATE ESTER HEME / Cytochrome b5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / restrained energy minimization
Model type detailsminimized average
AuthorsBanci, L. / Bertini, I. / Branchini, B.R. / Hajieva, P. / Spyroulias, G.A. / Turano, P.
CitationJournal: J.BIOL.INORG.CHEM. / Year: 2001
Title: Dimethyl propionate ester heme-containing cytochrome b5: structure and stability.
Authors: Banci, L. / Bertini, I. / Branchini, B.R. / Hajieva, P. / Spyroulias, G.A. / Turano, P.
History
DepositionSep 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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)11,4582
Polymers10,8141
Non-polymers6451
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -all calculated structures submitted
RepresentativeModel #1minimized average structure

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Components

#1: Protein cytochrome b5


Mass: 10813.908 Da / Num. of mol.: 1 / Fragment: soluble domain, RESIDUES 5-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: puc13 / Production host: Escherichia coli (E. coli) / Strain (production host): NM-522 / References: UniProt: P00173
#2: Chemical ChemComp-HDM / DIMETHYL PROPIONATE ESTER HEME


Mass: 644.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H36FeN4O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D NOESY-15N HMQC

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Sample preparation

Sample conditionsIonic strength: 100 mM potassium phosphate / pH: 7 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionClassification
DYANAstructure solution
Amber5refinement
RefinementMethod: restrained energy minimization / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers submitted total number: 1

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