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- PDB-1sh4: Solution structure of oxidized bovine microsomal cytochrome B5 Mu... -

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Basic information

Entry
Database: PDB / ID: 1sh4
TitleSolution structure of oxidized bovine microsomal cytochrome B5 Mutant V45H
ComponentsCytochrome b5
KeywordsELECTRON TRANSPORT / FIVE HELIX / FIVE SHEET / HEME RING
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 / heme 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 / Roll / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome b5
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodSOLUTION NMR / distance geomitry
AuthorsWu, H. / Zhang, Q.
CitationJournal: Protein Sci. / Year: 2004
Title: The comparative study on the solution structures of the oxidized bovine microsomal cytochrome b5 and mutant V45H
Authors: Zhang, Q. / Cao, C. / Wang, Z.Q. / Wang, Y.H. / Wu, H. / Huang, Z.X.
History
DepositionFeb 25, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 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 29, 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)10,1312
Polymers9,5141
Non-polymers6161
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 30structures with acceptable covalent geometry
RepresentativeModel #30lowest energy

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Components

#1: Protein Cytochrome b5


Mass: 9514.396 Da / Num. of mol.: 1 / Fragment: residues 3-84 / Mutation: V45H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / 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
1212D TOCSY
131DQF-COSY
1422D NOESY
1522D TOCSY
162DQF-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
13.0mM90% H2O/10% D2O
23.0mM100% D2O
Sample conditionsIonic strength: 25mM PHOSPHATE BUFFER / pH: 7.00 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Peter Guntertstructure solution
VNMR6.1BMike Carlislecollection
XEASYTai-he Xia and Chrisrian Barteldata analysis
Amber6Peter Kollmanrefinement
RefinementMethod: distance geomitry / Software ordinal: 1
Details: A total of 1682 NOE distance constraints, 24 Stereo-specific assignments constraints and 209 pseudocontact shift constraints were used in structure calculation
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 30 / Conformers submitted total number: 30

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