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- PDB-3dmr: STRUCTURE OF DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS AT PH 7.0 -

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Basic information

Entry
Database: PDB / ID: 3dmr
TitleSTRUCTURE OF DMSO REDUCTASE FROM RHODOBACTER CAPSULATUS AT PH 7.0
ComponentsDMSO REDUCTASE
KeywordsOXIDOREDUCTASE / DMSO / MOLYBDOPTERIN / PH 7
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
: / OXYGEN ATOM / Chem-PGD / Dimethyl sulfoxide/trimethylamine N-oxide reductase
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE MAPS FROM OXIDISED STRUCTURE (BNL-5270) / Resolution: 2.5 Å
AuthorsMcalpine, A.S. / Bailey, S.
Citation
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.
#1: 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 25, 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_conn_type / 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.conn_type_id / _struct_conn.id / _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_conn_type.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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DMSO REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1306
Polymers89,5251
Non-polymers1,6055
Water8,413467
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.450, 80.450, 229.110
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


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


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


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 33.9 %
Description: DIFFERENCE MAPS PICKED OUT CHANGES FROM OXIDIZED STRUCTURE
Crystal growpH: 7
Details: 0.1M CITRATE BUFFER, PH 4.8 - 5.2 20 - 3% PEG 4000 20% ETHANOL. CRYSTALS SOAKED IN 0.1M MES. PH 7.0 BEFORE DATA COLLECTION. CRYSTALS WERE SOAKED IN 0.1M MES BUFFER AT PH 7.0 FOR 10 MINUTES ...Details: 0.1M CITRATE BUFFER, PH 4.8 - 5.2 20 - 3% PEG 4000 20% ETHANOL. CRYSTALS SOAKED IN 0.1M MES. PH 7.0 BEFORE DATA COLLECTION. CRYSTALS WERE SOAKED IN 0.1M MES BUFFER AT PH 7.0 FOR 10 MINUTES BEFORE DATA COLLECTION.
PH range: 4.8-5.2
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: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 21981 / % possible obs: 83.8 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 5.7
Reflection shellResolution: 2.5→2.67 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 3.2 / % possible all: 76.3
Reflection
*PLUS
Num. measured all: 55133 / Rmerge(I) obs: 0.097

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: DIFFERENCE MAPS FROM OXIDISED STRUCTURE (BNL-5270)
Resolution: 2.5→20 Å / Cross valid method: USE OF SINGLE FREE R SET / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1144 5 %EVERY 20TH
Rwork0.181 ---
obs-27981 83.8 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6422 0 95 467 6984
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.004
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.3

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