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- PDB-1lj0: Structure of quintuple mutant of the rat outer mitocondrial cytoc... -

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Basic information

Entry
Database: PDB / ID: 1lj0
TitleStructure of quintuple mutant of the rat outer mitocondrial cytochrome b5.
ComponentsCytochrome B5 outer mitochondrial membrane isoform
KeywordsELECTRON TRANSPORT / CYTOCHROME / HEME / protein engineering
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 / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsCowley, A.B. / Altuve, A. / Kuchment, O. / Terzyan, S. / Zhang, X.C. / Rivera, M. / Benson, D.
CitationJournal: Biochemistry / Year: 2002
Title: Toward engineering the stability and hemin binding properties of microsomal cytochromes b5 into rat outer mitochondrial cytochrome b5: Examining the influence of residues 25 and 71.
Authors: Cowley, A.B. / Altuve, A. / Kuchment, O. / Terzyan, S. / Zhang, X.C. / Rivera, M. / Benson, D.
History
DepositionApr 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 16, 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 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)44,23611
Polymers41,6974
Non-polymers2,5397
Water3,441191
1
A: Cytochrome B5 outer mitochondrial membrane isoform
B: Cytochrome B5 outer mitochondrial membrane isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1306
Polymers20,8492
Non-polymers1,2824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cytochrome B5 outer mitochondrial membrane isoform
C: Cytochrome B5 outer mitochondrial membrane isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0824
Polymers20,8492
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cytochrome B5 outer mitochondrial membrane isoform
D: Cytochrome B5 outer mitochondrial membrane isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1065
Polymers20,8492
Non-polymers1,2573
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cytochrome B5 outer mitochondrial membrane isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0653
Polymers10,4241
Non-polymers6412
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)22,0824
Polymers20,8492
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2820 Å2
ΔGint-55 kcal/mol
Surface area10830 Å2
MethodPISA
6
A: Cytochrome B5 outer mitochondrial membrane isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0894
Polymers10,4241
Non-polymers6653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.753, 50.854, 167.397
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: 10424.323 Da / Num. of mol.: 4 / Fragment: water soluble domain / Mutation: A18S, I25L, I32L, L47R, L71S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PET11A / 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


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


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.03 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, MG ACETATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19 mg/mlprotein1drop
232 %(w/v)PEG1reservoir
30.2 Mmagnesium acetate1reservoir
40.1 MPIPES1reservoirpH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 8, 2002 / Details: Osmic multilayer mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 23729 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 33.02 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.78 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2215 / % possible all: 94.7
Reflection shell
*PLUS
% possible obs: 94.7 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 1ICC

1icc


Resolution: 2→23 Å / Isotropic thermal model: Overall anisotropic B factor / Cross valid method: R free / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: USED MAXIMUM LIKELIHOOD TARGET FOR AMPLITUDES
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1474 6.2 %Random
Rwork0.207 ---
all-23656 --
obs-21562 90.2 %-
Solvent computationBsol: 49.18 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 34.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.222 Å2--
2---6.698 Å2-
3---6.92 Å2
Refinement stepCycle: LAST / Resolution: 2→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 175 191 3187
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.61
Refinement
*PLUS
Num. reflection obs: 20088 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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