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- PDB-1h5n: DMSO REDUCTASE MODIFIED BY THE PRESENCE OF DMS AND AIR -

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Basic information

Entry
Database: PDB / ID: 1h5n
TitleDMSO REDUCTASE MODIFIED BY THE PRESENCE OF DMS AND AIR
ComponentsDimethyl sulfoxide/trimethylamine N-oxide reductase
KeywordsOXIDOREDUCTASE / REDUCTASE / DMSO / DMS / 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 / : / Dimethylsulfoxide Reductase; domain 2 / Dimethylsulfoxide Reductase, domain 2 / Rossmann fold - #740 ...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 / Barwin-like endoglucanases - #20 / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / 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
: / Chem-PGD / Dimethyl sulfoxide/trimethylamine N-oxide reductase
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBailey, S. / Adams, B. / Smith, A.T. / Richards, R.L. / Lowe, D.J. / Bray, R.C.
CitationJournal: Biochemistry / Year: 2001
Title: Reactions of Dimethyl Sulphoxide Reductase in the Presence of Dimethylsulphide and the Structure of the Dimethylsulphide-Modified Enzyme
Authors: Bray, R.C. / Adams, B. / Smith, A.T. / Richards, R.L. / Lowe, D.J. / Bailey, S.
History
DepositionMay 22, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2002Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2Nov 6, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_nat / struct_ref / 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 / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...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_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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AH" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)182,38810
Polymers179,0502
Non-polymers3,3388
Water22,2311234
1
A: Dimethyl sulfoxide/trimethylamine N-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1945
Polymers89,5251
Non-polymers1,6694
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)91,1945
Polymers89,5251
Non-polymers1,6694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.800, 116.100, 230.400
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: (0.03318, -0.07431, -0.99668), (0.51529, -0.8532, 0.08076), (-0.85637, -0.51626, 0.00999)
Vector: 45.3751, 86.18323, 33.0743)

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Components

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


Mass: 89524.945 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-6MO / MOLYBDENUM(VI) ION


Mass: 95.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mo
#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.: 1234 / 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.

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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: 2.57 Å3/Da / Density % sol: 45 %
Crystal growpH: 7.5
Details: 0.1M HEPES BUFFER, PH 7.5, 2M AMMONIUM SULPHATE, 4% PEG 400
Crystal grow
*PLUS
Temperature: 20-22 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMTris1droppH8.0
2100 mMNa+-Hepes1reservoirpH7.5
32 Mammonium sulfate1reservoir
43-4 %PEG4001reservoir

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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: 2→38 Å / Num. obs: 105657 / % possible obs: 83.7 % / Redundancy: 2.6 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 11.3
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.071 / Mean I/σ(I) obs: 9 / % possible all: 49.2
Reflection
*PLUS
Num. measured all: 277682
Reflection shell
*PLUS
% possible obs: 49.2 % / Mean I/σ(I) obs: 9

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E5V

1e5v


Resolution: 2→20 Å / SU B: 3.3 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.16
RfactorNum. reflection% reflectionSelection details
Rfree0.209 5290 5 %SAME AS PREVIOUS MODEL
Rwork0.158 ---
obs-100172 83.7 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11744 0 200 1234 13178
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
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
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.7

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