[English] 日本語
Yorodumi
- PDB-8ed4: Structure of the complex between the arsenite oxidase and its nat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ed4
TitleStructure of the complex between the arsenite oxidase and its native electron acceptor cytochrome c552 from Pseudorhizobium sp. str. NT-26
Components
  • AroA
  • AroB
  • C-type cytochrome c552
KeywordsELECTRON TRANSPORT / Complex
Function / homology
Function and homology information


arsenate reductase (azurin) / oxidoreductase complex / molybdopterin cofactor binding / 3 iron, 4 sulfur cluster binding / NADH dehydrogenase activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / heme binding / metal ion binding / membrane
Similarity search - Function
Arsenite oxidase subunit AioB/Iodate reductase subunit IdrB, small subunit / Arsenite oxidase subunit AioA/Iodate reductase subunit IdrA, large subunit / Arsenite oxidase subunit AioA/Iodate reductase subunit IdrA, 3Fe-4S cluster / Rieske 3Fe-4S / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 ...Arsenite oxidase subunit AioB/Iodate reductase subunit IdrB, small subunit / Arsenite oxidase subunit AioA/Iodate reductase subunit IdrA, large subunit / Arsenite oxidase subunit AioA/Iodate reductase subunit IdrA, 3Fe-4S cluster / Rieske 3Fe-4S / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / : / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
MOLYBDENUM(IV) ION / FE3-S4 CLUSTER / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-MGD / OXYGEN ATOM / C-type cytochrome c552 / AroA / AroB
Similarity search - Component
Biological speciesPseudorhizobium banfieldiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMaher, M.J. / Poddar, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: The structure of the complex between the arsenite oxidase from Pseudorhizobium banfieldiae sp. strain NT-26 and its native electron acceptor cytochrome c 552.
Authors: Poddar, N. / Santini, J.M. / Maher, M.J.
History
DepositionSep 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AroA
B: AroB
I: C-type cytochrome c552
C: AroA
D: AroB
J: C-type cytochrome c552
E: AroA
F: AroB
K: C-type cytochrome c552
G: AroA
H: AroB
L: C-type cytochrome c552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)505,02043
Polymers493,81312
Non-polymers11,20731
Water31,5081749
1
A: AroA
B: AroB
I: C-type cytochrome c552
C: AroA
D: AroB
J: C-type cytochrome c552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,26920
Polymers246,9066
Non-polymers5,36214
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: AroA
F: AroB
K: C-type cytochrome c552
G: AroA
H: AroB
L: C-type cytochrome c552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,75123
Polymers246,9066
Non-polymers5,84517
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.400, 126.560, 148.020
Angle α, β, γ (deg.)90.00, 107.81, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 3 types, 12 molecules ACEGBDFHIJKL

#1: Protein
AroA / Arsenite oxidase large subunit AioA [3Fe-4S] cluster / Mo-molybdopterin cofactor-binding active site


Mass: 93250.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudorhizobium banfieldiae (bacteria) / Gene: aroA, aioA, NT26_p10030 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VAL8, arsenate reductase (azurin)
#2: Protein
AroB


Mass: 17466.205 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudorhizobium banfieldiae (bacteria) / Gene: aroB / Production host: Escherichia coli (E. coli) / References: UniProt: Q6VAL9
#3: Protein
C-type cytochrome c552


Mass: 12736.475 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudorhizobium banfieldiae (bacteria) / Gene: cytC, NT26_p10031 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2TV05

-
Non-polymers , 10 types, 1780 molecules

#4: Chemical
ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#5: Chemical
ChemComp-4MO / MOLYBDENUM(IV) ION


Mass: 95.940 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mo
#6: Chemical
ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe3S4
#7: Chemical
ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O
#8: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#9: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#12: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1749 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium chloride, 0.1 M HEPES pH 7.3, 18% (w/v) PEG 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2.25→49.23 Å / Num. obs: 214836 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.998 / Net I/σ(I): 11.4
Reflection shellResolution: 2.25→2.29 Å / Num. unique obs: 10599 / CC1/2: 0.915

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AAY,1CO6

4aay

1co6


Resolution: 2.25→49.23 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.886 / SU B: 6.761 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.38 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23015 10062 5.1 %RANDOM
Rwork0.18101 ---
obs0.1835 188208 92.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.397 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20.02 Å2
2--0.42 Å20 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 2.25→49.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33256 0 632 1749 35637
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01334940
X-RAY DIFFRACTIONr_bond_other_d0.0020.01731126
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.65947541
X-RAY DIFFRACTIONr_angle_other_deg1.241.58472306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.66654363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.79622.7341902
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.214155521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.96315217
X-RAY DIFFRACTIONr_chiral_restr0.0630.24402
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0240063
X-RAY DIFFRACTIONr_gen_planes_other0.0020.027404
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8991.21317308
X-RAY DIFFRACTIONr_mcbond_other0.8981.21317307
X-RAY DIFFRACTIONr_mcangle_it1.5411.81521635
X-RAY DIFFRACTIONr_mcangle_other1.5411.81521636
X-RAY DIFFRACTIONr_scbond_it0.8541.2417632
X-RAY DIFFRACTIONr_scbond_other0.8541.2417633
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4941.83525847
X-RAY DIFFRACTIONr_long_range_B_refined3.08613.48640098
X-RAY DIFFRACTIONr_long_range_B_other3.08613.48740099
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 270 -
Rwork0.208 5517 -
obs--36.53 %

+
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