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- PDB-1cjc: STRUCTURE OF ADRENODOXIN REDUCTASE OF MITOCHONDRIAL P450 SYSTEMS -

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Basic information

Entry
Database: PDB / ID: 1cjc
TitleSTRUCTURE OF ADRENODOXIN REDUCTASE OF MITOCHONDRIAL P450 SYSTEMS
ComponentsPROTEIN (ADRENODOXIN REDUCTASE)
KeywordsOXIDOREDUCTASE / FLAVOENZYME / MAD ANALYSIS / 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 / NADPH:adrenodoxin oxidoreductase, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsZiegler, G.A. / Vonrhein, C. / Schulz, G.E.
Citation
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.
#1: 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
DepositionApr 12, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 17, 2013Group: Structure summary
Revision 1.4Nov 27, 2019Group: Advisory / Data collection / Database references
Category: citation / diffrn_source / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (ADRENODOXIN REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1462
Polymers50,3601
Non-polymers7861
Water10,503583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.810, 62.530, 78.370
Angle α, β, γ (deg.)90.00, 106.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (ADRENODOXIN REDUCTASE) / ADR / NADPH: ADRENODOXIN OXIDOREDUCTASE


Mass: 50360.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COFACTOR FAD IS NON-COVALENTLY BOUND / Source: (gene. exp.) Bos taurus (cattle) / Tissue: STEROIDOGENIC TISSUES
Description: EXPRESSION IN E.COLI WAS INCREASED BY COEXPRESSION OF THE HSP60-CHAPERONE SYSTEM
Cellular location: MITOCHONDRIAL MATRIX / Organelle: MITOCHONDRIAMitochondrion / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08165, adrenodoxin-NADP+ reductase
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 2.82 Å3/Da / Density % sol: 56 %
Crystal growpH: 6.5
Details: DROPLET: 4 MG/ML PROTEIN, 8% PEG8000, 5% GLYCEROL, 100 MM CALCIUM ACETATE, 50 MM SODIUM-CACODYLATE PH 6.5. RESERVOIR: 12 % PEG8000, 100 MM CALCIUM ACETATE, 50 MM SODIUM CACODYLATE PH 6.5.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDUnitCommon nameCrystal-IDSol-ID
1mg/mlprotein1drop
2mMsodium cacodylate1drop
3mMcalcium acetate1drop
4%(w/v)PEG80001drop
5%(v/v)glycerol1drop
6%(w/v)PEG80001reservoir
7mMsodium cacodylate1reservoir
8mMcalcium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.71→34 Å / Num. obs: 56738 / % possible obs: 93 % / Redundancy: 4.7 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.049 / Net I/σ(I): 10.8
Reflection shellResolution: 1.71→1.8 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.236 / % possible all: 76
Reflection shell
*PLUS
% possible obs: 76 %

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Processing

Software
NameVersionClassification
SHARPphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.7→18 Å / SU B: 2.5 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2892 5 %RANDOM
Rwork0.188 ---
obs-54650 94.5 %-
Displacement parametersBiso mean: 28.4 Å2
Refinement stepCycle: LAST / Resolution: 1.7→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 53 583 4141
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
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_it1.6
X-RAY DIFFRACTIONp_mcangle_it2.3
X-RAY DIFFRACTIONp_scbond_it2
X-RAY DIFFRACTIONp_scangle_it3
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

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