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- PDB-1e6e: ADRENODOXIN REDUCTASE/ADRENODOXIN COMPLEX OF MITOCHONDRIAL P450 S... -

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Basic information

Entry
Database: PDB / ID: 1e6e
TitleADRENODOXIN REDUCTASE/ADRENODOXIN COMPLEX OF MITOCHONDRIAL P450 SYSTEMS
Components
  • ADRENODOXINAdrenal ferredoxin
  • NADPH\:ADRENODOXIN OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / FLAVOENZYME / ELECTRON TRANSFERASE / [2FE-2S]FERREDOXIN / ADRENODOXIN / ELECTRON TRANSPORT / COMPLEX
Function / homologyAdrenodoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-like superfamily / Electron transport from NADPH to Ferredoxin / Endogenous sterols / Pregnenolone biosynthesis / Beta-grasp domain superfamily / Adrenodoxin / Mitochondrial iron-sulfur cluster biogenesis / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. ...Adrenodoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-like superfamily / Electron transport from NADPH to Ferredoxin / Endogenous sterols / Pregnenolone biosynthesis / Beta-grasp domain superfamily / Adrenodoxin / Mitochondrial iron-sulfur cluster biogenesis / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / FAD/NAD(P)-binding domain / Adrenodoxin family, iron-sulfur binding region signature. / Ferredoxin-NADP+ reductase, adrenodoxin-type / Pyridine nucleotide-disulphide oxidoreductase / 2Fe-2S iron-sulfur cluster binding domain / FAD/NAD(P)-binding domain superfamily / adrenodoxin-NADP+ reductase / NADPH-adrenodoxin reductase activity / hormone biosynthetic process / ubiquinone biosynthetic process / ferredoxin-NADP+ reductase activity / steroid biosynthetic process / cellular response to forskolin / cholesterol metabolic process / 2 iron, 2 sulfur cluster binding / cellular response to cAMP / mitochondrial inner membrane / flavin adenine dinucleotide binding / NADP binding / oxidation-reduction process / protein C-terminus binding / mitochondrial matrix / electron transfer activity / oxidoreductase activity / protein homodimerization activity / mitochondrion / metal ion binding / Adrenodoxin, mitochondrial / NADPH:adrenodoxin oxidoreductase, mitochondrial
Function and homology information
Specimen sourceBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.3 Å resolution
AuthorsMueller, J.J. / Lapko, A. / Bourenkov, G. / Ruckpaul, K. / Heinemann, U.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Adrenodoxin Reductase-Adrenodoxin Complex Structure Suggests Electron Transfer Path in Steroid Biosynthesis.
Authors: Mueller, J.J. / Lapko, A. / Bourenkov, G. / Ruckpaul, K. / Heinemann, U.
#1: Journal: To be Published
Title: X-Ray Structure of Bovine Adrenodoxin Reductase -Adrenodoxin Complex at 2.5 A Resolution: The First Three-Dimensional Structure of a Complex of Two Components of the Steroidogenic Electron Transport System in Adrenal Cortex Mitochondria
Authors: Mueller, J.J. / Lapko, A. / Bourenkov, G. / Mueller, E.C. / Otto, A. / Ruckpaul, K. / Heinemann, U.
#2: Journal: Proteins: Struct.,Funct., Genet. / Year: 1997
Title: Preparation and Crystallization of a Cross-Linked Complex of Bovine Adrenodoxin and Adrenodoxin Reductase
Authors: Lapko, A. / Mueller, A. / Heese, O. / Ruckpaul, K. / Heinemann, U.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 15, 2000 / Release: Aug 9, 2001
RevisionDateData content typeGroupProviderType
1.0Aug 9, 2001Structure modelrepositoryInitial release
1.1Sep 18, 2013Structure modelData collection / Derived calculations / Other / Refinement description / Structure summary / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH\:ADRENODOXIN OXIDOREDUCTASE
B: ADRENODOXIN
C: NADPH\:ADRENODOXIN OXIDOREDUCTASE
D: ADRENODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,18713
Polyers128,7844
Non-polymers2,4039
Water4,936274
1
A: NADPH\:ADRENODOXIN OXIDOREDUCTASE
B: ADRENODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6427
Polyers64,3922
Non-polymers1,2505
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4380
ΔGint (kcal/M)-57.4
Surface area (Å2)24320
MethodPISA
2
C: NADPH\:ADRENODOXIN OXIDOREDUCTASE
D: ADRENODOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5466
Polyers64,3922
Non-polymers1,1534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)4330
ΔGint (kcal/M)-70.0
Surface area (Å2)23900
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)92.210, 92.210, 607.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP 65 2 2

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Components

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Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein/peptide NADPH\:ADRENODOXIN OXIDOREDUCTASE / AR / ADRENODOXIN REDUCTASE / FERREDOXIN--NADP(+) REDUCTASE FERREDOXIN REDUCTASE / ADR / ADRENODOXIN REDUCTASE


Mass: 50360.410 Da / Num. of mol.: 2
Details: COVALENT CROSSLINK BETWEEN LYS27 OF ADR AND ASP39 OF ADX
Source: (gene. exp.) BOS TAURUS (cattle) / Tissue: STEROIDOGENIC TISSUES / Cell: MITOCHONDRION / Cellular location: ATTACHED TO INNER MITOCHONDRIAL MEMBRANE / Organ: ADRENAL GLAND / Organelle: MITOCHONDRIAL MATRIX / Plasmid name: PBAR1607 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P08165, ferredoxin-NADP+ reductase, adrenodoxin-NADP+ reductase
#2: Protein/peptide ADRENODOXIN / Adrenal ferredoxin / ADRENAL FERREDOXIN / FERREDOXIN-1 / HEPATO-FERREDOXIN / ADX / A DRENODOXIN


Mass: 14031.734 Da / Num. of mol.: 2
Details: COVALENT CROSSLINK BETWEEN LYS27 OF ADR AND ASP39 OF ADX
Mutation: YES / Source: (gene. exp.) BOS TAURUS (cattle) / Tissue: STEROIDOGENIC TISSUES / Cell: MITOCHONDRION / Organ: ADRENAL GLAND / Organelle: MITOCHONDRIAL MATRIX / Plasmid name: PKKHC, PMIXT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P00257

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Non-polymers , 4 types, 283 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Formula: C27H33N9O15P2 / Flavin adenine dinucleotide / Comment: FAD *YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Formula: SO4 / Sulfate
#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Formula: Fe2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Formula: H2O / Water

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Details

Compound detailsCHAIN B, D ENGINEERED MUTATION SER1GLY REDUCED ADRENODOXIN + NADP(+) = OXIDIZED ADRENODOXIN + NADPH ...CHAIN B, D ENGINEERED MUTATION SER1GLY REDUCED ADRENODOXIN + NADP(+) = OXIDIZED ADRENODOXIN + NADPH THE COVALENT CROSSLINK BETWEEN ASP39CG OF ADX AND LYS27NZ OF ADR WAS MEDIATED BY 1-ETHYL-3-(3-DIMETHYLAMINOPROPYL) CARBODIIMIDE (EDC) ADRENODOXIN TRANSFER ELECTRONS FROM ADRENODOXIN REDUCTASE TO THE CHOLESTEROL SIDE CHAIN CLEAVAGE CYTOCHROME P450
Sequence detailsFIRST 32 RESIDUES OF ADR SWISS-PROT SEQUENCE REFER TO A MITOCHONDRIAL LEADER SEQUENCE THAT WAS ...FIRST 32 RESIDUES OF ADR SWISS-PROT SEQUENCE REFER TO A MITOCHONDRIAL LEADER SEQUENCE THAT WAS CLEAVED WHEN CLONED. FIRST 58 RESIDUES OF ADX SWISS-PROT PRECURSOR SEQUENCE WERE CLEAVED WHEN CLONED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.9 / Density percent sol: 57 %
Crystal growpH: 7.4
Details: HANGING DROP VAPOR-DIFFUSION AT 4 DEGR. 0.5MM COMPLEX IN 100MMTRIS-HCL, PH 7.4, 0.9M AMMONIUMSULFATE.
Crystal grow
*PLUS
Temp: 4 ℃ / Method: vapor diffusion, hanging drop
Details: Lapko, A., (1997) Proteins: Struct.,Funct., Genet., 28, 289.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDDetails
11 mMcomplex1drop
2100 mMTris-HCl1droppH7.4
31.9 Mammonium sulfate1drop
41.9 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 1 kelvins
SourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.046
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Collection date: Apr 15, 1999
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.046 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 26.3 Å2 / D resolution high: 2.3 Å / D resolution low: 2 Å / Number obs: 55229 / Rsym value: 0.069 / NetI over sigmaI: 18.5 / Redundancy: 3.7 % / Percent possible obs: 79.1
Reflection shellHighest resolution: 2.3 Å / Lowest resolution: 2.4 Å / MeanI over sigI obs: 11 / Rsym value: 0.11 / Percent possible all: 56
Reflection
*PLUS
Number measured all: 201839 / Rmerge I obs: 0.069
Reflection shell
*PLUS
Percent possible obs: 56 / Rmerge I obs: 0.12

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSphasing
CNS1.0refinement
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1AYF AND 1CJC
R Free selection details: RANDOM / Data cutoff high absF: 4745426 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 26.9964 / Solvent model param ksol: 0.348512
Displacement parametersB iso mean: 30.4 Å2 / Aniso B11: 0.49 Å2 / Aniso B12: 4.19 Å2 / Aniso B13: 0 Å2 / Aniso B22: 0.49 Å2 / Aniso B23: 0 Å2 / Aniso B33: -0.99 Å2
Least-squares processR factor R free: 0.268 / R factor R free error: 0.005 / R factor R work: 0.222 / R factor obs: 0.222 / Highest resolution: 2.3 Å / Lowest resolution: 19.97 Å / Number reflection R free: 2791 / Number reflection obs: 55229 / Percent reflection R free: 5.1 / Percent reflection obs: 79.1
Refine analyzeLuzzati coordinate error free: 0.37 Å / Luzzati coordinate error obs: 0.29 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.3 Å / Luzzati sigma a obs: 0.2 Å
Refine hist #LASTHighest resolution: 2.3 Å / Lowest resolution: 19.97 Å
Number of atoms included #LASTProtein: 8699 / Nucleic acid: 0 / Ligand: 139 / Solvent: 274 / Total: 9112
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.244
X-RAY DIFFRACTIONc_mcangle_it2.155
X-RAY DIFFRACTIONc_scbond_it1.829
X-RAY DIFFRACTIONc_scangle_it2.854
Refine LS shellHighest resolution: 2.3 Å / R factor R free: 0.348 / R factor R free error: 0.02 / R factor R work: 0.249 / Lowest resolution: 2.44 Å / Number reflection R free: 300 / Number reflection R work: 6049 / Total number of bins used: 6 / Percent reflection R free: 4.7 / Percent reflection obs: 55.9
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_BREAK.TOP
X-RAY DIFFRACTION2FAD.PARFAD.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.223 / Percent reflection R free: 5
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.220
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.993
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
Refine LS shell
*PLUS
Highest resolution: 2.3 Å

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