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

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Basic information

Entry
Database: PDB / ID: 1icc
TitleRAT OUTER MITOCHONDRIAL MEMBRANE CYTOCHROME B5
ComponentsCYTOCHROME B5 OUTER MITOCHONDRIAL MEMBRANE ISOFORM
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 / 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 Å
AuthorsTerzyan, S. / Zhang, X.
CitationJournal: Biochemistry / Year: 2001
Title: Probing the differences between rat liver outer mitochondrial membrane cytochrome b5 and microsomal cytochromes b5.
Authors: Altuve, A. / Silchenko, S. / Lee, K.H. / Kuczera, K. / Terzyan, S. / Zhang, X. / Benson, D.R. / Rivera, M.
History
DepositionMar 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 1.4Aug 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

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME B5 OUTER MITOCHONDRIAL MEMBRANE ISOFORM
B: CYTOCHROME B5 OUTER MITOCHONDRIAL MEMBRANE ISOFORM
C: CYTOCHROME B5 OUTER MITOCHONDRIAL MEMBRANE ISOFORM
D: CYTOCHROME B5 OUTER MITOCHONDRIAL MEMBRANE ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,56711
Polymers40,0284
Non-polymers2,5397
Water4,468248
1
A: CYTOCHROME B5 OUTER MITOCHONDRIAL MEMBRANE ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6724
Polymers10,0071
Non-polymers6653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYTOCHROME B5 OUTER MITOCHONDRIAL MEMBRANE ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6232
Polymers10,0071
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CYTOCHROME B5 OUTER MITOCHONDRIAL MEMBRANE ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6483
Polymers10,0071
Non-polymers6412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CYTOCHROME B5 OUTER MITOCHONDRIAL MEMBRANE ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6232
Polymers10,0071
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
B: CYTOCHROME B5 OUTER MITOCHONDRIAL MEMBRANE ISOFORM
hetero molecules

C: CYTOCHROME B5 OUTER MITOCHONDRIAL MEMBRANE ISOFORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2715
Polymers20,0142
Non-polymers1,2573
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2800 Å2
ΔGint-55 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.904, 51.315, 167.419
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 OUTER MITOCHONDRIAL MEMBRANE ISOFORM


Mass: 10006.988 Da / Num. of mol.: 4 / Fragment: WATER SOLUBLE DOMAIN / Mutation: A18S, I32L, L47R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell: HEPATOCYTE / Organ: LIVER / Plasmid: PET 11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P04166
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000 Magnesium Acetate PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
Temperature: 5 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
127 %(w/v)PEG80001reservoir
20.2 Mmagnesium acetate1reservoir
30.1 MPIPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 2001 / Details: Osmic Blue Optics
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 24230 / Num. obs: 23878 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2324 / % possible all: 98.9
Reflection shell
*PLUS
% possible obs: 98.9 % / Num. unique obs: 2324

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Processing

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

1awp


Resolution: 2→50 Å / Isotropic thermal model: Anisotropic overall B-Factor / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber / Details: Used maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1494 6.7 %Random
Rwork0.196 ---
all0.23 23878 --
obs0.22 22023 91.4 %-
Solvent computationBsol: 53.34 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.354 Å20 Å20 Å2
2--0.155 Å20 Å2
3---5.199 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 175 248 3210
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.61
X-RAY DIFFRACTIONc_mcbond_it1.35
X-RAY DIFFRACTIONc_mcangle_it2.181
X-RAY DIFFRACTIONc_scbond_it2.06
X-RAY DIFFRACTIONc_scangle_it3.2
LS refinement shellResolution: 2→2.02 Å / Total num. of bins used: 29
RfactorNum. reflection% reflection
Rfree0.326 43 7 %
Rwork0.278 571 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3heme.paramheme.top
X-RAY DIFFRACTION4ion.paramion.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 6.7 % / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_scangle_it / Dev ideal: 3.2
LS refinement shell
*PLUS
Highest resolution: 2 Å / Rfactor Rfree: 0.326 / % reflection Rfree: 7 % / Rfactor Rwork: 0.278

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