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- PDB-1eue: RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5 -

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Basic information

Entry
Database: PDB / ID: 1eue
TitleRAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5
ComponentsCYTOCHROME B5
KeywordsELECTRON TRANSPORT / CYTOCHROME / HEME
Function / homology
Function and homology information


Phase I - Functionalization of compounds / nitric-oxide synthase complex / ubiquinol-cytochrome-c reductase activity / nitrite reductase (NO-forming) activity / enzyme activator activity / nitric oxide biosynthetic process / mitochondrial outer membrane / intracellular membrane-bounded organelle / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome b5 type B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOganesyan, V. / Zhang, X.
CitationJournal: FARADAY DISC.CHEM.SOC / Year: 2001
Title: Modulation of redox potential in electron transfer proteins: effects of complex formation on the active site microenvironment of cytochrome b5.
Authors: Wirtz, M. / Oganesyan, V. / Zhang, X. / Studer, J. / Rivera, M.
History
DepositionApr 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 19, 2014Group: Database references
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME B5
B: CYTOCHROME B5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9254
Polymers19,6922
Non-polymers1,2332
Water1,58588
1
A: CYTOCHROME B5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4622
Polymers9,8461
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYTOCHROME B5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4622
Polymers9,8461
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.230, 70.770, 72.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYTOCHROME B5 /


Mass: 9845.826 Da / Num. of mol.: 2 / Fragment: WATER SOLUBLE DOMAIN / Mutation: V45I, V61I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: HEPATOCYTE
Cellular location: OUTER MITOCHONDRIAL MEMBRANEMitochondrion
Organ: LIVER / Organelle: MITOCHONDRIAMitochondrion / Plasmid: PET 11A / Cellular location (production host): PERIPLASMIC SPACE / Production host: Escherichia coli (E. coli) / References: UniProt: P04166
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20% PEG 8000, 0.2 M magnesium acetate, 0.1 M PIPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Method: vapor diffusion
Details: drop solution is mixed 1:1 by volume with precipitant solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
220 %(w/v)PEG80001reservoirprecipitant
30.2 Mmagnesium acetate1reservoirprecipitant
40.1 MPIPES1reservoirprecipitant

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 15, 2000 / Details: OSMIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→24.2 Å / Num. obs: 21091 / % possible obs: 93 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.6
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.8 / % possible all: 91.8
Reflection shell
*PLUS
% possible obs: 91.8 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AWP

1awp


Resolution: 1.8→11.93 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1103526.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1040 4.9 %RANDOM
Rwork0.197 ---
obs0.197 21091 93.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.14 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1-13.48 Å20 Å20 Å2
2---7.24 Å20 Å2
3----6.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.8→11.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 0 86 88 1562
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.98
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 148 4.9 %
Rwork0.297 2867 -
obs--81.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4HEAM.PARHEAM.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98

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