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- PDB-4dmr: REDUCED DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS WITH BOUND DMS... -

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Basic information

Entry
Database: PDB / ID: 4dmr
TitleREDUCED DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS WITH BOUND DMSO SUBSTRATE
ComponentsDMSO REDUCTASE
KeywordsOXIDOREDUCTASE / DMSO / MOLYBDOPTERIN / SUBSTRATE BOUND
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 / molybdopterin cofactor binding / periplasmic space / metal ion binding
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
MOLYBDENUM(IV) ION / OXYGEN ATOM / Chem-PGD / Dimethyl sulfoxide/trimethylamine N-oxide reductase
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE MAPS USING OXIDISED STRUCTURE / Resolution: 1.9 Å
AuthorsMcalpine, A.S. / Bailey, S.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: The high resolution crystal structure of DMSO reductase in complex with DMSO.
Authors: McAlpine, A.S. / McEwan, A.G. / Bailey, S.
#1: Journal: J.Biol.Inorg.Chem. / Year: 1997
Title: Molybdenum Active Centre of Dmso Reductase from Rhodobacter Capsulatus: Crystal Structure of the Oxidised Enzyme at 1.82-A Resolution and the Dithionite-Reduced Enzyme at 2.8-A Resolution
Authors: Mcalpine, A.S. / Mcewan, A.G. / Shaw, A. / Bailey, S.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Preliminary Crystallographic Studies of Dimethylsulfoxide Reductase from Rhodobacter Capsulatus
Authors: Bailey, S. / Mcalpine, A.S. / Duke, E.M.H. / Benson, N. / Mcewan, A.G.
History
DepositionApr 30, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)91,1506
Polymers89,4831
Non-polymers1,6675
Water8,539474
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.970, 80.970, 230.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DMSO REDUCTASE /


Mass: 89482.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus (bacteria) / Cellular location: PERIPLASM / Strain: H123 / References: UniProt: Q52675

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Non-polymers , 5 types, 479 molecules

#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-4MO / MOLYBDENUM(IV) ION


Mass: 95.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mo
#4: Chemical ChemComp-O / OXYGEN ATOM / Oxygen


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsSTRUCTURE HAS DMSO (SUBSTRATE) BOUND AT THE ACTIVE SITE. THE ACTIVE SITE IS IN THE MO(IV) REDUCED STATE.

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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: 2.11 Å3/Da / Density % sol: 35.1 %
Crystal growpH: 5.5
Details: 0.1M CITRATE BUFFER, PH 4.8 - 5.2 20 - 3% PEG 4000 20% ETHANOL, pH 5.5 A FEW UL OF NEAT DMS (DIMETHYL SULFIDE) WAS ADDED TO THE DROP CONTAINING THE CRYSTAL IMMEDIATELY BEFORE DATA COLLECTION.
PH range: 4.8-5.2
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion
Details: Bailey, S., (1996) Acta Crystallogr.,Sect.D, 52, 194.
PH range low: 5.6 / PH range high: 5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
124-28 %PEG40001reservoir
20.1 Msodium citrate1reservoir
320 %ethanol1reservoir
47 mg/mlprotein1drop
55 mMsodium phosphate1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 3, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→17.3 Å / Num. obs: 58725 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 6
Reflection shellResolution: 1.9→2.03 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 2.3 / % possible all: 96.6
Reflection
*PLUS
Num. measured all: 227149
Reflection shell
*PLUS
% possible obs: 90.5 %

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: DIFFERENCE MAPS USING OXIDISED STRUCTURE
Starting model: OXIDISED STRUCTURE FOR DIFFERENCES IN DIFFERENCE MAP

Resolution: 1.9→20 Å / Cross valid method: USE OF SINGLE FREE R SET / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.19617 3033 5 %EVERY 20TH
Rwork0.15986 ---
obs-58725 96.6 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6422 0 98 539 7059
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 58725 / Rfactor obs: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_deg1.5

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