[English] 日本語
Yorodumi
- PDB-1e61: OXIDIZED DMSO REDUCTASE EXPOSED TO HEPES - Structure II BUFFER -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1.0E+61
TitleOXIDIZED DMSO REDUCTASE EXPOSED TO HEPES - Structure II BUFFER
ComponentsDimethyl sulfoxide/trimethylamine N-oxide reductase
KeywordsOXIDOREDUCTASE / REDUCTASE / DMSO / MOLYBDOPTERIN
Function / homology
Function and homology information


respiratory dimethylsulfoxide reductase / trimethylamine-N-oxide reductase / trimethylamine-N-oxide reductase (cytochrome c) activity / molybdenum ion binding / molybdopterin cofactor binding / anaerobic respiration / outer membrane-bounded periplasmic space / electron transfer activity
Similarity search - Function
Dimethylsulfoxide Reductase; domain 3 / Dimethylsulfoxide Reductase, domain 3 / Molybdopterin guanine dinucleotide-containing S/N-oxide reductase / Molybdopterin oxidoreductase, N-terminal / Trimethylamine-N-oxide reductase-like, molybdopterin-binding domain / Molybdopterin oxidoreductase N-terminal domain / : / Rossmann fold - #740 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 ...Dimethylsulfoxide Reductase; domain 3 / Dimethylsulfoxide Reductase, domain 3 / Molybdopterin guanine dinucleotide-containing S/N-oxide reductase / Molybdopterin oxidoreductase, N-terminal / Trimethylamine-N-oxide reductase-like, molybdopterin-binding domain / Molybdopterin oxidoreductase N-terminal domain / : / Rossmann fold - #740 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Prokaryotic molybdopterin oxidoreductases signature 2. / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Alpha-Beta Complex / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MOLYBDENUM (IV)OXIDE / Chem-PGD / Dimethyl sulfoxide/trimethylamine N-oxide reductase
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBailey, S. / Bennett, B. / Adams, B. / Smith, A.T. / Bray, R.C.
CitationJournal: Biochemistry / Year: 2000
Title: Reversible Dissociation of Thiolate Ligands from Molybdenum in an Enzyme of the Dimethyl Sulfoxide Reductase Family
Authors: Bray, R.C. / Adams, B. / Smith, A.T. / Bennett, B. / Bailey, S.
History
DepositionAug 6, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_nat / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_organism_scientific / _entity_src_nat.strain / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_auth_seq_align_beg
Revision 1.4Oct 26, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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
Revision 1.5May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dimethyl sulfoxide/trimethylamine N-oxide reductase
C: Dimethyl sulfoxide/trimethylamine N-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,45410
Polymers179,0522
Non-polymers3,4028
Water13,818767
1
A: Dimethyl sulfoxide/trimethylamine N-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2275
Polymers89,5261
Non-polymers1,7014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: Dimethyl sulfoxide/trimethylamine N-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2275
Polymers89,5261
Non-polymers1,7014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.189, 118.141, 235.163
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.03048, -0.07809, -0.99648), (0.50523, -0.85901, 0.08277), (-0.86245, -0.50598, 0.01327)
Vector: 45.48826, 87.24242, 33.02237)

-
Components

#1: Protein Dimethyl sulfoxide/trimethylamine N-oxide reductase / TMAOR


Mass: 89525.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus (bacteria) / Cellular location: PERIPLASM
References: UniProt: Q52675, trimethylamine-N-oxide reductase, respiratory dimethylsulfoxide reductase
#2: Chemical
ChemComp-PGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE


Mass: 738.541 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24N10O13P2S2
#3: Chemical ChemComp-2MO / MOLYBDENUM (IV)OXIDE


Mass: 127.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: MoO2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREDUCES VARIOUS N-OXIDE AND SULFOXIDE COMPOUNDS INCLUDING TRIMETHYLAMINE N-OXIDE DURING ANAEROBIC ...REDUCES VARIOUS N-OXIDE AND SULFOXIDE COMPOUNDS INCLUDING TRIMETHYLAMINE N-OXIDE DURING ANAEROBIC GROWTH USING MOLYBDENUM (MOLYBDOPTERIN)AS COFACTOR.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 45 %
Crystal growpH: 7.5
Details: 0.1M HEPES BUFFER, PH 7.5 - 2M AMMONIUM SULPHATE 3-4% PEG 400
Crystal grow
*PLUS
Temperature: 20-22 ℃ / pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mMsodium phosphate1drop
3100 mMNa+ HEPES1reservoir
42 Mammonium sulfate1reservoir
53-4 %PEG4001reservoir
2enzyme1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 121768 / % possible obs: 78.2 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 5.4
Reflection shellResolution: 1.9→1.91 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2.8 / % possible all: 52.9
Reflection
*PLUS
Num. measured all: 367035

-
Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS

Resolution: 1.9→20 Å / SU B: 3.2 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.216 6085 5 %EVERY 20TH
Rwork0.178 ---
obs-115651 78.2 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11768 0 202 767 12737
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0290.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.030.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
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
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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