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- PDB-1tmo: TRIMETHYLAMINE N-OXIDE REDUCTASE FROM SHEWANELLA MASSILIA -

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Basic information

Entry
Database: PDB / ID: 1tmo
TitleTRIMETHYLAMINE N-OXIDE REDUCTASE FROM SHEWANELLA MASSILIA
ComponentsTRIMETHYLAMINE N-OXIDE REDUCTASE
KeywordsOXIDOREDUCTASE / TMAO REDUCTASE / OXOTRANSFERASE / MOLYBDOENZYME / MO-COFACTOR / MOLYBDENUM / BIS (MOLYBDOPTERIN GUANINE DINUCLEOTIDE)
Function / homology
Function and homology information


trimethylamine-N-oxide reductase / trimethylamine-N-oxide reductase (cytochrome c) activity / molybdenum ion binding / molybdopterin cofactor binding / periplasmic space
Similarity search - Function
Trimethylamine-N-oxide reductase TorA / Dimethylsulfoxide Reductase; domain 3 / Dimethylsulfoxide Reductase, domain 3 / 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. ...Trimethylamine-N-oxide reductase TorA / Dimethylsulfoxide Reductase; domain 3 / Dimethylsulfoxide Reductase, domain 3 / 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
GUANYLATE-O'-PHOSPHORIC ACID / MOLYBDENUM (IV)OXIDE / Trimethylamine-N-oxide reductase
Similarity search - Component
Biological speciesShewanella massilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsCzjzek, M. / Dos Santos, J.P. / Giordano, G. / Mejean, V.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of oxidized trimethylamine N-oxide reductase from Shewanella massilia at 2.5 A resolution.
Authors: Czjzek, M. / Dos Santos, J.P. / Pommier, J. / Giordano, G. / Mejean, V. / Haser, R.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Molecular Analysis of the Trimethylamine N-Oxide (Tmao) Reductase Respiratory System from a Shewanella Species
Authors: Dos Santos, J.P. / Iobbi-Nivol, C. / Couillault, C. / Giordano, G. / Mejean, V.
History
DepositionAug 3, 1998Processing site: BNL
Revision 1.0Mar 30, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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: TRIMETHYLAMINE N-OXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0904
Polymers92,4771
Non-polymers1,6133
Water9,098505
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.320, 140.700, 59.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein TRIMETHYLAMINE N-OXIDE REDUCTASE / TMAO REDUCTASE


Mass: 92476.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: MARINE BACTERIA, ISOLATED FROM THE FISH MULLUS SURMULETUS
Source: (natural) Shewanella massilia (bacteria) / Cellular location: PERIPLASM / References: UniProt: O87948, EC: 1.6.6.9
#2: Chemical ChemComp-2MD / GUANYLATE-O'-PHOSPHORIC ACID MONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,5,6,7,8A,9,10,10A-OCTAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL) ESTER / MOLYBDENUM COFACTOR,BIS (MOLYBDOPTERIN GUANINE DINUCLEOTIDE)


Mass: 742.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28N10O13P2S2
#3: Chemical ChemComp-2MO / MOLYBDENUM (IV)OXIDE


Mass: 127.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: MoO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 3.4 Å3/Da / Density % sol: 64 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
2100 mMcacodylate1reservoir
4200 mMcalcium acetate1reservoir
518 %(w/v)PEG80001reservoir
3sodium salt1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31
DetectorDate: Dec 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 15.2 Å2
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 25 Å / Num. obs: 37497 / % possible obs: 92 % / Rmerge(I) obs: 0.14
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.61 Å / % possible obs: 81 % / Num. unique obs: 4403 / Rmerge(I) obs: 0.48

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementResolution: 2.5→20 Å / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.5
Details: TWO REFINEMENTS WERE DONE IN PARALLEL: ONE WITH TEST-SET AND ONE WITHOUT. THE FINAL, GLOBAL R-FACTOR GIVEN INCLUDES ALL REFLECTIONS AND NOT ONLY THOSE OF THE WORKING SET.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2992 10 %RANDOM
Rwork0.182 ---
obs0.182 29986 90.5 %-
Displacement parametersBiso mean: 13.31 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 3 Å / Luzzati sigma a obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6255 0 97 504 6856
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.34
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.61 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.319 284 11.1 %
Rwork0.225 2564 -
obs--83.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARDNA.PROTOPDNA.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.34
LS refinement shell
*PLUS
Rfactor obs: 0.225

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