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- PDB-1e1k: ADRENODOXIN REDUCTASE in complex with NADP+ obtained by a soaking... -

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Basic information

Entry
Database: PDB / ID: 1e1k
TitleADRENODOXIN REDUCTASE in complex with NADP+ obtained by a soaking experiment
ComponentsADRENODOXIN REDUCTASE
KeywordsOXIDOREDUCTASE / NADP+ / FLAVOENZYME / ELECTRON TRANSFERASE
Function / homology
Function and homology information


adrenodoxin-NADP+ reductase / NADPH-adrenodoxin reductase activity / ubiquinone biosynthetic process / steroid biosynthetic process / electron transport chain / cholesterol metabolic process / flavin adenine dinucleotide binding / NADP binding / mitochondrial inner membrane / mitochondrion
Similarity search - Function
Ferredoxin-NADP+ reductase, adrenodoxin-type / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADPH:adrenodoxin oxidoreductase, mitochondrial
Similarity search - Component
Biological speciesBOVINE (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsZiegler, G.A. / Schulz, G.E.
Citation
Journal: Biochemistry / Year: 2000
Title: Crystal Structures of Adrenodoxin Reductase in Complex with Nadp+ and Nadph Suggesting a Mechanism for the Electron Transfer of an Enzyme Family
Authors: Ziegler, G.A. / Schulz, G.E.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: The Structure of Adrenodoxin Reductase of Mitochondrial P450 Systems: Electron Transfer for Steroid Biosynthesis
Authors: Ziegler, G.A. / Vonrhein, C. / Hanukoglu, I. / Schulz, G.E.
#2: Journal: FEBS Lett. / Year: 1999
Title: Chaperone-Assisted Expression of Authentic Bovine Adrenodoxin Reductase in Escherichia Coli
Authors: Vonrhein, C. / Schmidt, U. / Ziegler, G.A. / Schweiger, S. / Hanukoglu, I. / Schulz, G.E.
History
DepositionMay 9, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADRENODOXIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8893
Polymers50,3601
Non-polymers1,5292
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.900, 62.400, 78.200
Angle α, β, γ (deg.)90.00, 106.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ADRENODOXIN REDUCTASE /


Mass: 50360.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOVINE (cattle) / Tissue: STEROIDOGENIC TISSUES STEROIDOGENIC TISSUES / Cellular location: MITOCHONDRIAL MATRIX / Organelle: MITOCHONDRIAMitochondrion / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08165
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST 32 RESIDUES OF SWISS-PROT SEQUENCE REFER TO A MITOCHONDRIAL LEADER SEQUENCE THAT WAS DELETED ...FIRST 32 RESIDUES OF SWISS-PROT SEQUENCE REFER TO A MITOCHONDRIAL LEADER SEQUENCE THAT WAS DELETED WHEN CLONED. THIS STRUCTURE PROBABLY SHOWS AN INTERMEDIATE OF THE NADP BINDING PROCESS

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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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
25 %glycerol1drop
38 %(w/v)PEG80001drop
450 mMsodium cacodylate1dropBuffer C
5100 mMcalcium acetate1dropBuffer C
712 %(w/v)PEG80001reservoir
6Buffer C1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorDate: Jul 15, 1999
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 41174 / % possible obs: 100 % / Redundancy: 3.6 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.069 / Net I/σ(I): 10
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.33 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 26 Å / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.33

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Processing

SoftwareName: REFMAC / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CJC

1cjc


Resolution: 1.95→20 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 -5 %RANDOM
Rwork0.184 ---
obs-41105 100 %-
Displacement parametersBiso mean: 26.5 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 101 346 3952
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d0.024
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 29 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.4

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