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- PDB-1eu1: THE CRYSTAL STRUCTURE OF RHODOBACTER SPHAEROIDES DIMETHYLSULFOXID... -

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Basic information

Entry
Database: PDB / ID: 1eu1
TitleTHE CRYSTAL STRUCTURE OF RHODOBACTER SPHAEROIDES DIMETHYLSULFOXIDE REDUCTASE REVEALS TWO DISTINCT MOLYBDENUM COORDINATION ENVIRONMENTS.
ComponentsDIMETHYL SULFOXIDE REDUCTASE
KeywordsOXIDOREDUCTASE / Molybdenum / Molybdenum Cofactor / DMSO / Reductase / Molybdopterin / MGD
Function / homology
Function and homology information


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 / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / 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
: / : / alpha-D-glucopyranose / Chem-MGD / OXYGEN ATOM / Dimethyl sulfoxide/trimethylamine N-oxide reductase
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 Å
AuthorsLi, H.K. / Temple, K. / Rajagopalan, K.V. / Schindelin, H.
Citation
Journal: J.Am.Chem.Soc. / Year: 2000
Title: The 1.3 A Crystal Structure of Rhodobacter sphaeroides Dimethylsulfoxide Reductase Reveals Two Distinct Molybdenum Coordination Environments
Authors: Li, H.K. / Temple, K. / Rajagopalan, K.V. / Schindelin, H.
#1: Journal: Science / Year: 1996
Title: Crystal Structure of DMSO Reductase: Redox-linked Changes in Molybdopterin Coordination
History
DepositionApr 13, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionAug 2, 2000ID: 1CXS, 1CXT
Revision 1.0Aug 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIMETHYL SULFOXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,61912
Polymers85,0221
Non-polymers2,59611
Water18,7181039
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.176, 141.718, 59.812
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2006-

CD

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Components

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Protein / Sugars , 2 types, 4 molecules A

#1: Protein DIMETHYL SULFOXIDE REDUCTASE / DMSO REDUCTASE / DMSOR


Mass: 85022.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Production host: Bacteria (eubacteria)
References: UniProt: Q57366, Oxidoreductases; Acting on a sulfur group of donors; With unknown physiological acceptors
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 1047 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#6: Chemical ChemComp-6MO / MOLYBDENUM(VI) ION


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


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#8: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1039 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Hepes, Cadmium Chloride, Ammonium Sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 22.0K
Crystal
*PLUS
Density % sol: 52 %
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlenzyme1drop
210 mMTris1reservoir
31.65 Mammonium sulfate1reservoir
40.1 MHEPES1reservoir
510 mM1reservoirCdCl2

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC / Detector: CCD / Date: Feb 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 213176 / Num. obs: 191461 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 19.9
Reflection shellResolution: 1.3→1.35 Å / Rmerge(I) obs: 0.211 / Num. unique all: 12690 / % possible all: 60.2
Reflection
*PLUS
Highest resolution: 1.3 Å
Reflection shell
*PLUS
Highest resolution: 1.3 Å / % possible obs: 60.2 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.3→10 Å / σ(F): 0 / σ(I): 0
Stereochemistry target values: Victor S. Lamzin, Zbigniew Dauter, and Keith S. Wilson
Details: Maximum likelihood refinement including anisotropic temperature factors for all atoms.
RfactorNum. reflection% reflectionSelection details
Rfree0.145 4711 -Random
Rwork0.121 ---
all-195723 --
obs-191012 89.8 %-
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5885 0 154 1039 7078
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONREFMAC bond distance0.01
X-RAY DIFFRACTIONREFMAC bond angle expressed as a distance0.03
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.3 Å / σ(F): 0 / Rfactor obs: 0.121
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d0.03
LS refinement shell
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 1.36 Å / Rfactor Rfree: 0.187 / Rfactor obs: 0.161

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