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- PDB-4f82: X-ray crystal structure of a putative thioredoxin reductase from ... -

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Basic information

Entry
Database: PDB / ID: 4f82
TitleX-ray crystal structure of a putative thioredoxin reductase from Burkholderia cenocepacia
ComponentsThioredoxin Reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


glutathione-dependent peroxiredoxin / cell redox homeostasis / peroxidase activity
Similarity search - Function
Peroxiredoxin-5-like / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutathione-dependent peroxiredoxin
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: X-ray crystal structure of a putative thioredoxin reductase from Burkholderia cenocepacia
Authors: Fairman, J.W. / Davies, D.R. / Sankaran, B. / Staker, B.L. / Stewart, L.
History
DepositionMay 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)37,4032
Polymers37,4032
Non-polymers00
Water6,630368
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-9 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.650, 61.970, 69.810
Angle α, β, γ (deg.)90.000, 98.850, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

#1: Protein Thioredoxin Reductase


Mass: 18701.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: BceJ2315_33940, BCAL3456 / Production host: Escherichia coli (E. coli) / References: UniProt: B4E5Y6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.15 Å3/Da / Density % sol: 42.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 200 mM magnesium chloride, 25% PEG3350, 100 BIS-TRIS pH 5.50, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.977408 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977408 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 27247 / Num. obs: 26023 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.146 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 6.36
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.85-1.90.42.234686194895.5
1.9-1.950.3282.614489187496.6
1.95-2.010.2892.944414185296.6
2.01-2.070.273.254226176197
2.07-2.140.2343.694150172996.6
2.14-2.210.24.124013170097.5
2.21-2.290.165.13875160796.7
2.29-2.390.1675.053707156096.7
2.39-2.490.1326.013595150897.5
2.49-2.620.1276.343389140996.6
2.62-2.760.1156.783243134594.7
2.76-2.930.0987.853079128296.4
2.93-3.130.0789.412889120496.2
3.13-3.380.07410.572654110294.7
3.38-3.70.06612.12465100493.6
3.7-4.140.05713.06222691493.1
4.14-4.780.05914.44192879090.7
4.78-5.850.0613.53163465990.6
5.85-8.270.05712.98130350187.7
8.270.04216.7171527482.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIXdev_1048refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TP9

1tp9


Resolution: 1.85→46.099 Å / Occupancy max: 1 / Occupancy min: 0.05 / FOM work R set: 0.8489 / SU ML: 0.22 / σ(F): 1.35 / Phase error: 22.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2235 1299 4.99 %RANDOM
Rwork0.1756 ---
obs0.178 26008 95.49 %-
all-27247 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.45 Å2 / Biso mean: 14.3402 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 0 368 2854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142557
X-RAY DIFFRACTIONf_angle_d1.5243478
X-RAY DIFFRACTIONf_chiral_restr0.104402
X-RAY DIFFRACTIONf_plane_restr0.009457
X-RAY DIFFRACTIONf_dihedral_angle_d14.415900
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.92390.27571350.22412755289096
1.9239-2.01140.27751490.21022761291097
2.0114-2.11750.26161470.19182773292097
2.1175-2.25020.26271330.18822774290797
2.2502-2.42390.23491540.1822772292697
2.4239-2.66780.24441480.18012763291196
2.6678-3.05380.22751360.17552765290196
3.0538-3.84710.19941450.15422722286794
3.8471-46.0990.1641520.14662624277690
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)
15.7968-0.0009-0.65638.61480.32573.198-0.35530.3802-0.1844-0.6614-0.0512-0.01340.2349-0.4260.27020.17630.0112-0.00320.1773-0.05480.131413.12576.7203-12.801
20.16790.19160.32281.07960.49121.3082-0.01-0.00440.1999-0.07110.0378-0.0187-0.05740.0795-0.04140.05520.0005-0.00570.0715-0.00640.10720.099211.5918-15.9695
30.00020.0167-0.01972.0153-2.30932.64610.2497-0.4440.31740.31920.26380.6061-0.5392-0.3997-0.39910.28030.08370.00490.23130.00060.2723-18.695914.1154-20.3625
40.67090.24440.24860.96440.25481.0296-0.0370.02430.0412-0.04870.0283-0.0111-0.1176-0.06990.01010.07310.0093-0.02170.0738-0.00670.0762-6.13688.0483-10.5037
54.48290.73911.24896.20191.99174.2795-0.1934-0.0002-0.01420.2829-0.18580.19720.0881-0.43930.20750.08940.02060.02770.107-0.01570.1371-11.595413.16291.2113
60.6674-0.05770.2230.96250.1660.90550.0215-0.05140.0106-0.0078-0.0016-0.0624-0.0162-0.0071-0.01220.0637-0.0096-0.00680.04860.00920.057-2.13025.7681-7.9878
70.85980.12120.13871.06991.05412.1033-0.24970.1573-0.2621-0.23670.0792-0.20580.11480.23010.0320.2129-0.01690.04830.1095-0.02870.1368-1.8628-21.3427-24.6394
80.16410.393-0.45731.7554-1.61571.6083-0.02480.1948-0.3738-0.01480.22540.26440.2995-0.245-0.16990.4061-0.0402-0.0950.1737-0.01840.4418-13.8527-24.009-6.9904
90.58590.21940.36391.11580.6161.49570.0501-0.0319-0.1137-0.04110.02430.08420.12290.016-0.06470.12-0.0034-0.02880.06780.00160.0826-12.852-19.1332-23.486
101.62152.01110.94773.13292.011.6466-0.0577-0.0499-0.0239-0.0207-0.08130.19670.1897-0.08150.01340.23650.0236-0.07020.0084-0.02780.1222-15.9268-27.5161-25.422
111.04420.10990.02991.16250.0651.76820.00550.0067-0.0510.0007-0.0151-0.0541-0.0036-0.00720.01040.09510.0009-0.02050.0421-0.00410.0599-7.8125-11.8753-22.8457
120.8450.08670.28691.2170.41290.55970.06830.0043-0.0584-0.4479-0.0262-0.05660.0655-0.0138-0.04080.18490.01380.00650.0932-0.01370.0661-11.6164-20.7353-35.904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -2:2)A-2 - 2
2X-RAY DIFFRACTION2(chain A and resid 3:17)A3 - 17
3X-RAY DIFFRACTION3(chain A and resid 18:24)A18 - 24
4X-RAY DIFFRACTION4(chain A and resid 25:63)A25 - 63
5X-RAY DIFFRACTION5(chain A and resid 64:71)A64 - 71
6X-RAY DIFFRACTION6(chain A and resid 72:168)A72 - 168
7X-RAY DIFFRACTION7(chain B and resid 0:17)B0 - 17
8X-RAY DIFFRACTION8(chain B and resid 18:24)B18 - 24
9X-RAY DIFFRACTION9(chain B and resid 25:70)B25 - 70
10X-RAY DIFFRACTION10(chain B and resid 71:79)B71 - 79
11X-RAY DIFFRACTION11(chain B and resid 80:136)B80 - 136
12X-RAY DIFFRACTION12(chain B and resid 137:168)B137 - 168

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