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- PDB-1e18: TUNGSTEN-SUSBSTITUTED DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS -

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Basic information

Entry
Database: PDB / ID: 1.0E+18
TitleTUNGSTEN-SUSBSTITUTED DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS
ComponentsDMSO REDUCTASE.
KeywordsOXIDOREDUCTASE / REDUCTASE / DMSO / MOLYBDOPTERIN / MOLYBDENUM / TUNGSTEN
Function / homology
Function and homology information


trimethylamine-N-oxide reductase activity / 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 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 / Prokaryotic molybdopterin oxidoreductases signature 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 / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 / 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
OXO-TUNGSTEN(VI) / ETHANOL / Chem-PGD / Dimethyl sulfoxide/trimethylamine N-oxide reductase
Similarity search - Component
Biological speciesRHODOBACTER CAPSULATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2 Å
AuthorsBailey, S. / Stewart, L.J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Dimethylsulfoxide Reductase: An Enzyme Capable of Catalysis with Either Molybdenum or Tungsten at the Active Site
Authors: Stewart, L.J. / Bailey, S. / Bennett, B. / Charnock, J.M. / Garner, C.D. / Mcalpine, A.S.
History
DepositionApr 28, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 / _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.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.value / _struct_conn.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DMSO REDUCTASE.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3987
Polymers89,5831
Non-polymers1,8156
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)80.920, 80.920, 229.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DMSO REDUCTASE. / DIMETHYLSULFOXIDE REDUCTASE


Mass: 89583.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: TUNGSTEN SUBSTITUTED FOR MOLYBDENUM / Source: (natural) RHODOBACTER CAPSULATUS (bacteria) / Cellular location: PERIPLASM / Strain: H123 / References: UniProt: Q52675
#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.: 2 / Source method: obtained synthetically / Formula: C20H24N10O13P2S2
#3: Chemical ChemComp-6WO / OXO-TUNGSTEN(VI)


Mass: 199.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: OW
#4: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFOR THE RESIDUES LISTED IN THE SEQADV RECORDS THE DIFFERENCES WERE OBSERVED IN THE ELECTRON DENSITY ...FOR THE RESIDUES LISTED IN THE SEQADV RECORDS THE DIFFERENCES WERE OBSERVED IN THE ELECTRON DENSITY TO THE SWISSPROT SEQUENCE

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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: 2.1 Å3/Da / Density % sol: 34.4 %
Crystal growpH: 4.9
Details: 0.1M CITRATE BUFFER, PH 4.8 -5.2, 20 - 23% PEG 4000, 20% ETHANOL
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion / PH range low: 5.5 / PH range high: 4.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlenzyme1drop
20.1 Msodium citrate1drop
320 %ethanol1drop
410 %PEG40001drop
525 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorDate: Jul 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 51645 / % possible obs: 98 % / Redundancy: 4.5 % / Rsym value: 0.066 / Net I/σ(I): 9
Reflection shellResolution: 1.9→2.03 Å / Mean I/σ(I) obs: 4.2 / Rsym value: 0.157 / % possible all: 92.3
Reflection
*PLUS
Num. measured all: 233511 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 92.3 % / Rmerge(I) obs: 0.157

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.192 -5 %EVERY 20TH
Rwork0.142 ---
obs-51645 98 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5976 0 105 394 6475
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
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

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