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- PDB-2bt6: Ru(bpy)2(mbpy)-Modified Bovine Adrenodoxin -

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Basic information

Entry
Database: PDB / ID: 2bt6
TitleRu(bpy)2(mbpy)-Modified Bovine Adrenodoxin
ComponentsADRENODOXIN 1
KeywordsELECTRON TRANSPORT / RUTHENIUM(II) BIPYRIDYL COMPLEX / INTRAMOLECULAR ELECTRON TRANSFER / METAL-BINDING
Function / homology
Function and homology information


Mitochondrial iron-sulfur cluster biogenesis / Pregnenolone biosynthesis / Endogenous sterols / Electron transport from NADPH to Ferredoxin / hormone biosynthetic process / P450-containing electron transport chain / steroid biosynthetic process / respiratory electron transport chain / cholesterol metabolic process / electron transport chain ...Mitochondrial iron-sulfur cluster biogenesis / Pregnenolone biosynthesis / Endogenous sterols / Electron transport from NADPH to Ferredoxin / hormone biosynthetic process / P450-containing electron transport chain / steroid biosynthetic process / respiratory electron transport chain / cholesterol metabolic process / electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial matrix / protein homodimerization activity / mitochondrion / metal ion binding
Similarity search - Function
Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) ...Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / (4'-METHYL-2,2'BIPYRIDINE)BIS(2,2'-BIPYRIDINE) / Adrenodoxin, mitochondrial
Similarity search - Component
Biological speciesBOS TAURUS (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHalavaty, A. / Mueller, J.J. / Contzen, J. / Jung, C. / Hannemann, F. / Bernhardt, R. / Galander, M. / Lendzian, F. / Heinemann, U.
CitationJournal: Biochemistry / Year: 2006
Title: Light-Induced Reduction of Bovine Adrenodoxin Via the Covalently Bound Ruthenium(II) Bipyridyl Complex: Intramolecular Electron Transfer and Crystal Structure.
Authors: Halavaty, A. / Mueller, J.J. / Contzen, J. / Jung, C. / Hannemann, F. / Bernhardt, R. / Galander, M. / Lendzian, F. / Heinemann, U.
History
DepositionMay 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 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 / pdbx_struct_conn_angle / struct_conn
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 / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADRENODOXIN 1
B: ADRENODOXIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2687
Polymers23,6412
Non-polymers1,6285
Water3,801211
1
A: ADRENODOXIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6223
Polymers11,8201
Non-polymers8022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADRENODOXIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6464
Polymers11,8201
Non-polymers8263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.510, 56.970, 79.080
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 ADRENODOXIN 1 / BOVINE ADRENODOXIN / ADRENAL FERREDOXIN


Mass: 11820.351 Da / Num. of mol.: 2 / Fragment: RESIDUES 63-166
Source method: isolated from a genetically manipulated source
Details: COVALENT LINK BETWEEN CYS95 AND C39 ATOM OF RU(BPY)2(MBPY) PER EACH CHAIN IN ASYMMETRIC UNIT
Source: (gene. exp.) BOS TAURUS (cattle) / Organ: ADRENAL CORTEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00257
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-RUA / (4'-METHYL-2,2'BIPYRIDINE)BIS(2,2'-BIPYRIDINE)


Mass: 625.897 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H56N6Ru
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: TRANSFER ELECTRONS FROM ADRENODOXIN REDUCTASE TO THE CHOLESTEROL SIDE CHAIN CLEAVAGE CYTOCHROME P450

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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: 2.71 Å3/Da / Density % sol: 54.33 %
Crystal growpH: 7.4
Details: 30% PEG 4000, 10% GLYCEROL, 10MM TRIS, PH 7.4, 10MM MGCL2, 20 MG/ML PROTEIN

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.006321
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 16, 2003 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006321 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 35907 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.1
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.4 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AYF

1ayf


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.613 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.186 1822 5 %RANDOM
Rwork0.161 ---
obs0.163 34414 97.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2--0.6 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1605 0 87 211 1903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211876
X-RAY DIFFRACTIONr_bond_other_d0.0010.021573
X-RAY DIFFRACTIONr_angle_refined_deg4.6312.7272582
X-RAY DIFFRACTIONr_angle_other_deg0.81533650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4565210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78325.48882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.54615311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.404159
X-RAY DIFFRACTIONr_chiral_restr0.080.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02393
X-RAY DIFFRACTIONr_nbd_refined0.2140.2354
X-RAY DIFFRACTIONr_nbd_other0.1850.21613
X-RAY DIFFRACTIONr_nbtor_refined0.1970.2964
X-RAY DIFFRACTIONr_nbtor_other0.080.2980
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.66721103
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.05231686
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.684.51194
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8816890
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.273 137
Rwork0.222 2456
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.54442.325-0.208717.25799.079211.506-0.00620.3384-0.6888-0.0981-0.06420.08610.6667-0.08440.0703-0.0806-0.0026-0.0245-0.0115-0.05610.001313.072314.6095-4.8172
22.3847-0.41230.21624.96050.60983.35850.02360.1417-0.0196-0.23440.0105-0.0615-0.14380.1106-0.0341-0.1454-0.01370.0079-0.0531-0.0171-0.061519.247120.09941.1149
33.2249-0.3327-0.64152.9993-2.682210.3640.0508-0.02240.01990.1103-0.0894-0.2513-0.1320.41660.0387-0.1318-0.0051-0.0085-0.0853-0.0169-0.076924.943418.464110.3518
44.22490.15831.85182.81820.12173.95460.0745-0.3477-0.15660.2824-0.09560.25090.1224-0.46010.0211-0.0728-0.01390.048-0.0453-0.0088-0.041311.086318.902714.9027
53.00391.1461.43641.96531.12853.45910.06030.014-0.13990.01-0.04030.12030.1089-0.1057-0.0199-0.1468-0.00550.0243-0.0821-0.0204-0.086213.279816.18085.3537
62.1005-5.8833-1.567416.48833.880928.3925-0.1114-0.58750.83460.0035-0.1018-1.738-2.01931.67330.21320.175-0.2675-0.17970.27440.07720.208151.406919.959928.571
72.19061.331-0.69429.42320.48072.637-0.07020.01580.0276-0.2398-0.1402-0.6025-0.32140.4110.21040.0328-0.0986-0.05730.06970.070.017544.718815.058423.163
812.1457-3.63810.784.4331-1.84073.90890.12310.7358-0.1185-0.1874-0.3251-0.1709-0.07220.2610.2020.0081-0.0494-0.0536-0.02030.0276-0.074534.790316.941618.8071
94.7047-0.55131.10133.3098-0.5532.893-0.1454-0.380.23170.4862-0.0377-0.0257-0.45220.03780.18310.1136-0.0553-0.0391-0.03520.0031-0.06132.286416.715132.9317
102.38380.6776-0.49463.3216-0.79672.64750.0023-0.22650.18530.3519-0.1255-0.2614-0.53220.35940.12320.095-0.1205-0.0850.03120.0127-0.032941.408119.614929.4122
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 9
2X-RAY DIFFRACTION2A10 - 36
3X-RAY DIFFRACTION3A37 - 55
4X-RAY DIFFRACTION3A1109
5X-RAY DIFFRACTION4A56 - 90
6X-RAY DIFFRACTION5A91 - 108
7X-RAY DIFFRACTION5A1110
8X-RAY DIFFRACTION5B1111
9X-RAY DIFFRACTION6B5 - 9
10X-RAY DIFFRACTION7B10 - 36
11X-RAY DIFFRACTION8B37 - 55
12X-RAY DIFFRACTION8B1109
13X-RAY DIFFRACTION9B56 - 90
14X-RAY DIFFRACTION10B91 - 108
15X-RAY DIFFRACTION10B1110

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