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- PDB-2m33: Solution NMR structure of full-length oxidized microsomal rabbit ... -

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Basic information

Entry
Database: PDB / ID: 2m33
TitleSolution NMR structure of full-length oxidized microsomal rabbit cytochrome b5
ComponentsCytochrome b5
KeywordsELECTRON TRANSPORT / membrane protein / heme / HADDOCK
Function / homology
Function and homology information


heme binding / endoplasmic reticulum membrane / enzyme binding / metal ion binding / cytosol
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 / Roll / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome b5
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodSOLUTION NMR / distance geometry, torsion angle dynamics, simulated annealing
Model detailsminimized average structure, model1
Model type detailsminimized average
AuthorsSubramanian, V. / Ahuja, S. / Popovych, N. / Huang, R. / Le Clair, S.V. / Jahr, N. / Soong, R. / Xu, J. / Yamamoto, K. / Nanga, R.P. ...Subramanian, V. / Ahuja, S. / Popovych, N. / Huang, R. / Le Clair, S.V. / Jahr, N. / Soong, R. / Xu, J. / Yamamoto, K. / Nanga, R.P. / Im, S. / Waskell, L. / Ramamoorthy, A.
CitationJournal: To be Published
Title: NMR structure of full-length mammalian cytochrome b5
Authors: Ahuja, S. / Subramanian, V. / Popovych, N. / Huang, R. / Le Clair, S.V. / Jahr, N. / Soong, R. / Xu, J. / Yamamoto, K. / Nanga, R.P. / Im, S. / Waskell, L. / Ramamoorthy, A.
History
DepositionJan 8, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Structure summary
Revision 1.2Jun 14, 2023Group: 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_nmr_spectrometer / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)15,9872
Polymers15,3701
Non-polymers6161
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)23 / 50structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Cytochrome b5 /


Mass: 15370.223 Da / Num. of mol.: 1 / Fragment: UNP residues 1-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CYB5A, CYB5 / Plasmid: pSC / Production host: Escherichia coli (E. coli) / References: UniProt: P00169
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1332D 1H-1H NOESY
1423D HNCO
1523D HNCA
1623D HN(CA)CB
1723D HN(CO)CA
1813D 1H-15N NOESY
1913D 1H-15N TOCSY
11013D 1H-13C NOESY
11113D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
145 mM [U-2H] DPC, 5 w/v glycerol, 100 mM potassium phosphate, 0.001 mM DSS, 0.1-0.5 mM [U-13C; U-15N] Cytochrome b5 full-length, 0.1-0.5 mM heme, 90% H2O/10% D2O90% H2O/10% D2O
245 mM [U-2H] DPC, 5 w/v glycerol, 100 mM potassium phosphate, 0.001 mM DSS, 0.1-0.5 mM [U-13C; U-15N; U-2H] Cytochrome b5 full-length, 0.1-0.5 mM heme, 90% H2O/10% D2O90% H2O/10% D2O
345 mM [U-2H] DPC, 5 w/v glycerol, 100 mM potassium phosphate, 0.001 mM DSS, 0.1-0.5 mM Cytochrome b5 full-length, 0.1-0.5 mM heme, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
45 mMDPC-1[U-2H]1
5 w/vglycerol-21
90 %H2O-31
10 %D2O-4[U-2H]1
100 mMpotassium phosphate-51
0.001 mMDSS-61
mMCytochrome b5 full-length-7[U-13C; U-15N]0.1-0.51
mMheme-80.1-0.51
45 mMDPC-9[U-2H]2
5 w/vglycerol-102
90 %H2O-112
10 %D2O-12[U-2H]2
100 mMpotassium phosphate-132
0.001 mMDSS-142
mMCytochrome b5 full-length-15[U-13C; U-15N; U-2H]0.1-0.52
mMheme-160.1-0.52
45 mMDPC-17[U-2H]3
5 w/vglycerol-183
90 %H2O-193
10 %D2O-20[U-2H]3
100 mMpotassium phosphate-213
0.001 mMDSS-223
mMCytochrome b5 full-length-230.1-0.53
mMheme-240.1-0.53
Sample conditionsIonic strength: 100 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddarddata analysis
Sparky3.113Goddardpeak picking
HADDOCKAlexandre Bonvinrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: distance geometry, torsion angle dynamics, simulated annealing
Software ordinal: 1
NMR constraintsNOE constraints total: 1787 / NOE intraresidue total count: 377 / NOE long range total count: 485 / NOE medium range total count: 412 / NOE sequential total count: 513
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 23 / Maximum lower distance constraint violation: 0.12 Å / Maximum upper distance constraint violation: 0.18 Å
NMR ensemble rmsDistance rms dev: 0.32 Å / Distance rms dev error: 0.1 Å

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