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- PDB-1b5m: RAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5 -

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Basic information

Entry
Database: PDB / ID: 1b5m
TitleRAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5
ComponentsCYTOCHROME B5
KeywordsELECTRON TRANSPORT / CYTOCHROME / HEME
Function / homology
Function and homology information


Sphingolipid de novo biosynthesis / Phase I - Functionalization of compounds / nitric-oxide synthase complex / nitrite reductase (NO-forming) activity / ubiquinol-cytochrome-c reductase 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 ...: / 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: 2.7 Å
AuthorsRivera, M. / White, S.P. / Zhang, X.
CitationJournal: Biochemistry / Year: 1996
Title: 13C NMR spectroscopic and X-ray crystallographic study of the role played by mitochondrial cytochrome b5 heme propionates in the electrostatic binding to cytochrome c.
Authors: Rodriguez-Maranon, M.J. / Qiu, F. / Stark, R.E. / White, S.P. / Zhang, X. / Foundling, S.I. / Rodriguez, V. / Schilling 3rd., C.L. / Bunce, R.A. / Rivera, M.
History
DepositionNov 7, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _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)10,2222
Polymers9,6061
Non-polymers6161
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.000, 30.000, 219.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CYTOCHROME B5


Mass: 9605.570 Da / Num. of mol.: 1 / Fragment: WATER SOLUBLE DOMAIN
Source method: isolated from a genetically manipulated source
Details: FROM RAT OUTER MITOCHONDRIAL MEMBRANE / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: HEPATOCYTE / Cell line: BL21 / Cellular location: OUTER MITOCHONDRIAL MEMBRANE / Organ: LIVER / Organelle: MITOCHONDRION / Plasmid: PET 11A / Species (production host): Escherichia coli / Cellular location (production host): PERIPLASMIC SPACE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P04166
#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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growMethod: vapor diffusion with slow evaporation / pH: 6.5
Details: CRYSTALS WERE OBTAINED BY VAPOR DIFFUSION TOGETHER WITH SLOW EVAPORATION USING 20% PEG 8000 IN 0.1M SODIUM CACODYLATE (PH = 6.5 WITH 0.2 M MAGNESIUM ACETATE., vapor diffusion with slow evaporation
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
220 %PEG80001reservoir
30.1 Msodium cacodylate1reservoir
40.2 Mmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 18, 1996
RadiationMonochromator: DIAMOND C(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 3123 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 36 Å2 / Rsym value: 0.049 / Net I/σ(I): 1.5
Reflection shellResolution: 2.7→3.05 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1 / Rsym value: 0.088 / % possible all: 85
Reflection
*PLUS
Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 85 % / Rmerge(I) obs: 0.088

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Processing

Software
NameVersionClassification
MRCHKmodel building
TNT5Erefinement
FRAMBOdata reduction
SADIEdata reduction
SAINTdata scaling
MRCHKphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B5C

3b5c
PDB Unreleased entry


Resolution: 2.7→20 Å / Isotropic thermal model: TNT / σ(F): 0 / Stereochemistry target values: TNT
RfactorNum. reflection% reflection
Rwork0.22 --
Rfree-3123 -
all-3123 -
obs-3123 96 %
Solvent computationSolvent model: BSOL / Bsol: 99.7 Å2 / ksol: 0.79 e/Å3
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms676 0 43 0 719
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0167440.8
X-RAY DIFFRACTIONt_angle_deg2.910031.3
X-RAY DIFFRACTIONt_dihedral_angle_d204120
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.007232
X-RAY DIFFRACTIONt_gen_planes0.0121045
X-RAY DIFFRACTIONt_it4.996922
X-RAY DIFFRACTIONt_nbd0.0232510
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.012 / Weight: 5

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