[English] 日本語
Yorodumi
- PDB-3hyw: 3-D X-Ray structure of the sulfide:quinone oxidoreductase of the ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hyw
Title3-D X-Ray structure of the sulfide:quinone oxidoreductase of the hyperthermophilic bacterium Aquifex aeolicus in complex with decylubiquinone
ComponentsSulfide-quinone reductase
KeywordsOXIDOREDUCTASE / MONOTOPIC MEMBRANE PROTEIN / FLAVOPROTEIN / POLYSULFUR
Function / homology
Function and homology information


bacterial sulfide:quinone reductase / sulfide:quinone oxidoreductase activity / aerobic electron transport chain / NAD(P)H dehydrogenase (quinone) activity / quinone binding / nucleotide binding / identical protein binding / membrane
Similarity search - Function
: / FAD/NAD(P)-binding domain - #100 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
Chem-DCQ / FLAVIN-ADENINE DINUCLEOTIDE / HYDROSULFURIC ACID / octathiocane / Sulfide-quinone reductase
Similarity search - Component
Biological speciesAQUIFEX AEOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMarcia, M. / Ermler, U. / Peng, G.H. / Michel, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration
Authors: Marcia, M. / Ermler, U. / Peng, G.H. / Michel, H.
History
DepositionJun 23, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionJul 14, 2009ID: 3H28
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sulfide-quinone reductase
B: Sulfide-quinone reductase
C: Sulfide-quinone reductase
D: Sulfide-quinone reductase
E: Sulfide-quinone reductase
F: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,67662
Polymers285,4026
Non-polymers14,27456
Water20,4831137
1
A: Sulfide-quinone reductase
C: Sulfide-quinone reductase
E: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,58130
Polymers142,7013
Non-polymers6,88027
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sulfide-quinone reductase
D: Sulfide-quinone reductase
F: Sulfide-quinone reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,09432
Polymers142,7013
Non-polymers7,39329
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33870 Å2
ΔGint-505 kcal/mol
Surface area86610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.780, 154.010, 175.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Sugars , 2 types, 12 molecules ABCDEF

#1: Protein
Sulfide-quinone reductase / sulfide:quinone oxidoreductase


Mass: 47566.984 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) AQUIFEX AEOLICUS (bacteria) / Strain: VF5
References: UniProt: O67931, Oxidoreductases; Acting on a sulfur group of donors; With a quinone or similar compound as acceptor
#4: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 6 types, 1187 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-DCQ / 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione / decylubiquinone


Mass: 322.439 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H30O4
#5: Chemical
ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H2S
#6: Chemical
ChemComp-PS9 / octathiocane


Mass: 256.520 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: S8
#7: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1137 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsTHE SIDE CHAIN OF CYS156 AND CYS347 ARE EXTENDED TO FORM A PUTATIVE POLYSULFUR CHAIN. ONE SULFUR ...THE SIDE CHAIN OF CYS156 AND CYS347 ARE EXTENDED TO FORM A PUTATIVE POLYSULFUR CHAIN. ONE SULFUR ATOM OF THE CHAIN IS DESCRIBED AS LINKED TO THE CYS AND FORM A S-MERCAPTO-CYSTEINE, CSS. THE REST OF THE CHAIN TAKES THE FORM OF A CYCLOOCTASULFUR SPECIES PS9 IN SEVERAL MONOMERS AND MIGHT REPRESENT THE PRODUCT OF THE REACTION CATALYZED BY THE PROTEIN. H2S INDICATES A PUTATIVE S ATOM BRIDGING CYS124 AND FAD. THIS S ATOM IS POSSIBLY CONTRIBUTED BY THE SUBSTRATE OF THE PROTEIN, HYDROGEN SULFIDE. PLEASE REFER TO THE RELATED PUBLICATION FOR A MORE DETAILED DESCRIPTION OF THE PUTATIVE SULFUR LIGANDS OF THE SULFIDE:QUINONE OXIDOREDUCTASE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 4% PEG 400, 2M AMMONIUM SULFATE, 0.1M NA-ACETATE, PH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0015 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 28, 2008 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0015 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 194489 / % possible obs: 96.2 % / Redundancy: 4.74 % / Net I/σ(I): 13.17
Reflection shellResolution: 2→2.1 Å / Redundancy: 1.86 % / Mean I/σ(I) obs: 1.86 / % possible all: 76.7

-
Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3H27

3h27
PDB Unreleased entry


Resolution: 2→20.45 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.395 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2357 9757 5 %RANDOM
Rwork0.19972 ---
obs0.20152 184559 96.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.976 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2---0.74 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2→20.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20036 0 829 1137 22002
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02221462
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1512.0129130
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.36152568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29524.336858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.453153378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4211584
X-RAY DIFFRACTIONr_chiral_restr0.0710.23162
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215936
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.210677
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.214544
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.21541
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4241.513309
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.654220910
X-RAY DIFFRACTIONr_scbond_it1.0439822
X-RAY DIFFRACTIONr_scangle_it1.6284.58220
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 533 -
Rwork0.267 10293 -
obs--73.64 %

+
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