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- PDB-9h4t: Crystal Structure of TorA -

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Basic information

Entry
Database: PDB / ID: 9h4t
TitleCrystal Structure of TorA
ComponentsTrimethylamine-N-oxide reductase 1
KeywordsMETAL BINDING PROTEIN / molybdenum-containing cofactor / electron transfer
Function / homology
Function and homology information


trimethylamine-N-oxide reductase (cytochrome c) complex / trimethylamine-N-oxide reductase / trimethylamine-N-oxide reductase (cytochrome c) activity / anaerobic electron transport chain / regulation of pH / molybdenum ion binding / molybdopterin cofactor binding / anaerobic respiration / aerobic respiration / outer membrane-bounded periplasmic space / electron transfer activity
Similarity search - Function
Trimethylamine-N-oxide reductase TorA / 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 / : / Prokaryotic molybdopterin oxidoreductases signature 2. / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin dinucleotide-binding domain ...Trimethylamine-N-oxide reductase TorA / 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 / : / Prokaryotic molybdopterin oxidoreductases signature 2. / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
: / D-MALATE / DI(HYDROXYETHYL)ETHER / Chem-PGD / TRIETHYLENE GLYCOL / Trimethylamine-N-oxide reductase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsPanwar, A. / Martins, B.M. / Sommer, F. / Dobbek, H. / Iobbi-Nivol, C. / Jourlin-Castelli, C. / Leimkuehler, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2008-390540038 Germany
CitationJournal: Int J Mol Sci / Year: 2024
Title: Purification and Electron Transfer from Soluble c-Type Cytochrome TorC to TorA for Trimethylamine N-Oxide Reduction.
Authors: Panwar, A. / Martins, B.M. / Sommer, F. / Schroda, M. / Dobbek, H. / Iobbi-Nivol, C. / Jourlin-Castelli, C. / Leimkuhler, S.
History
DepositionOct 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trimethylamine-N-oxide reductase 1
B: Trimethylamine-N-oxide reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,80136
Polymers189,1362
Non-polymers6,66634
Water27,8151544
1
A: Trimethylamine-N-oxide reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,40123
Polymers94,5681
Non-polymers3,83322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Trimethylamine-N-oxide reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,40013
Polymers94,5681
Non-polymers2,83212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.662, 117.467, 100.053
Angle α, β, γ (deg.)90.00, 103.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Trimethylamine-N-oxide reductase 1 / TMAO reductase 1 / Trimethylamine oxidase 1


Mass: 94567.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: fusion with C-term His-tag / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: torA, b0997, JW0982 / Production host: Escherichia coli (E. coli)
References: UniProt: P33225, trimethylamine-N-oxide reductase

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Non-polymers , 7 types, 1578 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.: 4 / Source method: obtained synthetically / Formula: C20H24N10O13P2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-6MO / MOLYBDENUM(VI) ION


Mass: 95.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mo / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H6O5
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1544 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.85 Å3/Da / Density % sol: 56 % / Description: long parallelipide
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 60% PEG 1000, 150 mM di-sodium DL-malate, pH 5.0, 4 mM sodium fluoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 14, 2018
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.86→47.79 Å / Num. obs: 159613 / % possible obs: 90.88 % / Redundancy: 2.4 % / Biso Wilson estimate: 22.09 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.114 / Net I/σ(I): 7.45
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 2.4 % / Num. unique obs: 61348 / CC1/2: 0.609 / Rrim(I) all: 0.543 / % possible all: 88.7

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Processing

Software
NameVersionClassification
REFMACv1.0refinement
autoXDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→47.79 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.865 / SU B: 5.653 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28875 2101 1.3 %RANDOM
Rwork0.2351 ---
obs0.2358 157492 90.84 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.921 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0 Å2-0.23 Å2
2--2.31 Å20 Å2
3----1.83 Å2
Refinement stepCycle: LAST / Resolution: 1.86→47.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12507 0 424 1544 14475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01613279
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612181
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.78718002
X-RAY DIFFRACTIONr_angle_other_deg0.4211.56228052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7065.2561677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.098536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.541102074
X-RAY DIFFRACTIONr_chiral_restr0.0560.21882
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215632
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023152
X-RAY DIFFRACTIONr_mcbond_it4.8372.5236346
X-RAY DIFFRACTIONr_mcbond_other4.8332.5236346
X-RAY DIFFRACTIONr_mcangle_it5.8124.5217931
X-RAY DIFFRACTIONr_mcangle_other5.8124.5227932
X-RAY DIFFRACTIONr_scbond_it6.0182.9036933
X-RAY DIFFRACTIONr_scbond_other6.0182.9046934
X-RAY DIFFRACTIONr_scangle_other7.555.12710068
X-RAY DIFFRACTIONr_long_range_B_refined8.52427.115912
X-RAY DIFFRACTIONr_long_range_B_other8.46226.415456
LS refinement shellResolution: 1.863→1.911 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 147 -
Rwork0.348 11008 -
obs--85.99 %

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