[English] 日本語
Yorodumi
- PDB-2bt6: Ru(bpy)2(mbpy)-Modified Bovine Adrenodoxin -

+
Open data


ID or keywords:

Loading...

-
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 / Electron transport from NADPH to Ferredoxin / Endogenous sterols / Protein lipoylation / hormone biosynthetic process / P450-containing electron transport chain / steroid biosynthetic process / cholesterol metabolic process / respiratory electron transport chain ...Mitochondrial iron-sulfur cluster biogenesis / Pregnenolone biosynthesis / Electron transport from NADPH to Ferredoxin / Endogenous sterols / Protein lipoylation / hormone biosynthetic process / P450-containing electron transport chain / steroid biosynthetic process / cholesterol metabolic process / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transport chain / electron transfer activity / mitochondrial matrix / protein homodimerization activity / mitochondrion
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 (domestic 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 2.0Sep 2, 2026Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_contact_author / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_validate_chiral / struct_conn / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _pdbx_contact_author.country / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,2127
Polymers23,6412
Non-polymers1,5715
Water3,801211
1
A: ADRENODOXIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5943
Polymers11,8201
Non-polymers7732
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADRENODOXIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6184
Polymers11,8201
Non-polymers7983
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

-
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 (domestic 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: 597.675 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H28N6Ru
#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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more