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- PDB-3r9u: Thioredoxin-disulfide reductase from Campylobacter jejuni. -

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Basic information

Entry
Database: PDB / ID: 3r9u
TitleThioredoxin-disulfide reductase from Campylobacter jejuni.
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / thioredoxin-disulfide reductase / FAD
Function / homology
Function and homology information


thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / nucleotide binding / cytoplasm
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.36 Å
AuthorsOsipiuk, J. / Zhou, M. / Kwon, K. / Anderson, K.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Thioredoxin-disulfide reductase from Campylobacter jejuni.
Authors: Osipiuk, J. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin reductase
B: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5225
Polymers67,8882
Non-polymers1,6333
Water1,51384
1
A: Thioredoxin reductase
hetero molecules

A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5846
Polymers67,8882
Non-polymers1,6954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area6910 Å2
ΔGint-25 kcal/mol
Surface area26420 Å2
MethodPISA
2
B: Thioredoxin reductase
hetero molecules

B: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4604
Polymers67,8882
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area6590 Å2
ΔGint-30 kcal/mol
Surface area26370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.006, 163.571, 66.876
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Thioredoxin reductase


Mass: 33944.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: subsp. jejuni NCTC 11168 / Gene: Cj0146c, trxB / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q0PBZ1, thioredoxin-disulfide reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES buffer, 30% PEG-4000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 13, 2010
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.36→36.1 Å / Num. all: 35153 / Num. obs: 35153 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 63 Å2 / Rmerge(I) obs: 0.105 / Χ2: 1.625 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.36-2.46.70.8412.0917631.02499.7
2.4-2.447.10.76717081.071100
2.44-2.497.20.717571.093100
2.49-2.547.30.61417171.13699.9
2.54-2.67.30.50117331.131100
2.6-2.667.30.45417501.174100
2.66-2.727.30.37817441.281100
2.72-2.87.30.31117441.38899.9
2.8-2.887.30.28617281.43299.9
2.88-2.977.20.22517431.577100
2.97-3.087.20.19517411.744100
3.08-3.27.20.15517641.85399.9
3.2-3.357.10.12617651.90699.9
3.35-3.5370.10517502.026100
3.53-3.756.90.09417582.081100
3.75-4.036.70.08217572.06799.9
4.03-4.446.60.07417752.031100
4.44-5.086.40.07217882.05499.9
5.08-6.46.20.07218032.45100
6.4-505.50.06118652.33297.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.36→36.1 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.925 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 16.025 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 1749 5 %RANDOM
Rwork0.1933 ---
all0.196 35055 --
obs0.196 35055 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 95.96 Å2 / Biso mean: 51.7942 Å2 / Biso min: 28.49 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å20 Å20 Å2
2---2.19 Å20 Å2
3---4.27 Å2
Refinement stepCycle: LAST / Resolution: 2.36→36.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4644 0 110 84 4838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224936
X-RAY DIFFRACTIONr_angle_refined_deg1.8062.0066669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1725653
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85125.497191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.88915894
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9821519
X-RAY DIFFRACTIONr_chiral_restr0.110.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213625
X-RAY DIFFRACTIONr_mcbond_it0.9331.53118
X-RAY DIFFRACTIONr_mcangle_it1.75624972
X-RAY DIFFRACTIONr_scbond_it3.03431818
X-RAY DIFFRACTIONr_scangle_it4.8634.51682
LS refinement shellResolution: 2.358→2.419 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 138 -
Rwork0.268 2344 -
all-2482 -
obs-2482 95.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7765-0.28230.62670.2132-0.31510.5277-0.05250.1816-0.063-0.0506-0.0274-0.05910.02740.01970.07980.05540.0150.01520.1477-0.05030.0558-6.973334.277818.375
21.0170.0829-0.43121.5657-0.86450.6610.11450.17830.0901-0.23140.02710.08370.1133-0.0998-0.14160.17110.0202-0.02220.08110.04170.104133.19658.815319.4418
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 501
2X-RAY DIFFRACTION2B-1 - 501

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