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- PDB-6bwt: 2.45 Angstrom Resolution Crystal Structure Thioredoxin Reductase ... -

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Basic information

Entry
Database: PDB / ID: 6bwt
Title2.45 Angstrom Resolution Crystal Structure Thioredoxin Reductase from Francisella tularensis.
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Thioredoxin Reductase
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / 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 superfamily
Similarity search - Domain/homology
Thioredoxin reductase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.45 Angstrom Resolution Crystal Structure Thioredoxin Reductase from Francisella tularensis.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: Thioredoxin reductase
D: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,67723
Polymers137,2164
Non-polymers1,46219
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13860 Å2
ΔGint-351 kcal/mol
Surface area48220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.299, 112.587, 167.044
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEUAA2 - 3145 - 317
21ALAALALEULEUBB2 - 3145 - 317
12ASNASNASPASPAA3 - 3156 - 318
22ASNASNASPASPCC3 - 3156 - 318
13ASNASNASNASNAA3 - 3136 - 316
23ASNASNASNASNDD3 - 3136 - 316
14ASNASNASNASNBB3 - 3136 - 316
24ASNASNASNASNCC3 - 3136 - 316
15ASNASNLEULEUBB3 - 3146 - 317
25ASNASNLEULEUDD3 - 3146 - 317
16ASNASNLEULEUCC3 - 3146 - 317
26ASNASNLEULEUDD3 - 3146 - 317

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Thioredoxin reductase


Mass: 34303.902 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: trxB, FTT_0489c / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5NHG5, thioredoxin-disulfide reductase (NADPH)
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.91 Å3/Da / Density % sol: 35.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 7.7 mG/mL, 0.25M Sodium chloride, 0.01M Tris-HCL pH 8.3; Screen: Clssics II (F8), 0.2M Ammonium sulfate, 0.1M HEPES (pH 7.5), 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2010 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 41167 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 51.4 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.029 / Rrim(I) all: 0.067 / Rsym value: 0.06 / Χ2: 1.014 / Net I/σ(I): 25.6
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2009 / CC1/2: 0.717 / Rpim(I) all: 0.363 / Rrim(I) all: 0.818 / Rsym value: 0.73 / Χ2: 0.994 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TDE

1tde


Resolution: 2.45→29.52 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 18.487 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.751 / ESU R Free: 0.296 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25217 2074 5 %RANDOM
Rwork0.21524 ---
obs0.21708 39025 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 65.212 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å20 Å20 Å2
2--1.68 Å20 Å2
3---0.72 Å2
Refinement stepCycle: 1 / Resolution: 2.45→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8306 0 71 247 8624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0198502
X-RAY DIFFRACTIONr_bond_other_d0.0010.027973
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.95911502
X-RAY DIFFRACTIONr_angle_other_deg0.85318508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.04851104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.41925.983351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.621151476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.9941521
X-RAY DIFFRACTIONr_chiral_restr0.0790.21358
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.029473
X-RAY DIFFRACTIONr_gen_planes_other0.0210.021560
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1254.2324431
X-RAY DIFFRACTIONr_mcbond_other2.1254.2324430
X-RAY DIFFRACTIONr_mcangle_it3.4886.3385530
X-RAY DIFFRACTIONr_mcangle_other3.4886.3385531
X-RAY DIFFRACTIONr_scbond_it2.2984.654071
X-RAY DIFFRACTIONr_scbond_other2.2434.6174020
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6916.7735895
X-RAY DIFFRACTIONr_long_range_B_refined6.41650.4389020
X-RAY DIFFRACTIONr_long_range_B_other6.38150.338986
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A153300.12
12B153300.12
21A153360.12
22C153360.12
31A156360.1
32D156360.1
41B156460.1
42C156460.1
51B152320.12
52D152320.12
61C153600.11
62D153600.11
LS refinement shellResolution: 2.451→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 174 -
Rwork0.271 2685 -
obs--96.69 %
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)
13.86050.161-2.11441.904-0.27065.153-0.13730.0088-0.3302-0.0035-0.0131-0.01270.2065-0.4180.15040.0238-0.0239-0.01720.05320.02340.083319.480714.902635.497
26.2484-0.5823-3.9122.469-1.36025.39560.13150.0458-0.15250.19220.00690.0741-0.2312-0.1849-0.13850.24670.0159-0.00570.03760.0570.100924.42946.350621.8077
30.70480.8346-2.03191.1137-2.57026.16340.184-0.19180.0680.305-0.0689-0.1333-0.80780.1956-0.11510.72860.08030.00330.5287-0.00740.804324.808950.252629.4353
42.94720.5273-0.94520.1783-0.57962.33430.0117-0.3412-0.15850.0135-0.038-0.0315-0.0304-0.01250.02640.07290.0163-0.01830.0530.02870.081632.74619.007838.6498
52.0396-1.1767-0.38253.905-0.54983.05790.10580.10210.2858-0.459-0.1371-0.2729-0.11610.29080.03130.08790.02590.05610.08670.07760.109555.36324.136717.9017
62.72-1.0184-3.62483.10520.52237.24740.4269-0.02170.19570.0656-0.28460.3197-0.38650.3315-0.14230.2405-0.03260.06390.0596-0.01380.103149.84-9.580533.6276
76.72731.0258-0.57347.03370.7784.14360.2606-0.65890.19230.4137-0.0238-0.9926-0.44971.1153-0.23680.1839-0.135-0.03930.4849-0.0290.164162.3518-8.805737.8745
82.98420.6432-0.84132.3056-0.36692.45430.0421-0.35120.1880.089-0.0389-0.1652-0.02310.3445-0.00320.05780.0107-0.01720.09330.01690.127150.312620.900530.1778
92.405-1.3727-0.13433.0991-0.51441.2983-0.2649-0.03650.0938-0.01190.0495-0.4415-0.02090.1060.21550.1727-0.0175-0.06010.01320.01310.121760.0319-0.06637.6487
104.8871-1.7326-2.13736.29913.60486.7521-0.11280.5686-0.146-0.1007-0.3360.5431-0.113-0.47550.44880.08520.0427-0.07550.107-0.07030.136230.104419.161612.1265
118.20311.5105-2.19046.6072-0.2967.342-0.04691.2219-0.8013-1.0384-0.68140.90630.338-0.54560.72830.27540.113-0.18540.3213-0.2770.311427.669612.27843.1024
121.2037-0.66810.19112.46930.2471.1843-0.22140.1441-0.0919-0.11010.1376-0.08880.0736-0.14740.08380.3255-0.03430.00020.13130.01480.158148.1679-3.61373.2377
136.910.74390.11492.43940.85033.5393-0.0357-0.6945-0.18650.57340.09910.4836-0.1386-0.6877-0.06340.29760.05490.14760.3030.15440.27429.271-20.736821.0454
144.8637-0.27750.44112.5112-1.72111.58540.1667-0.4953-0.0997-0.308-0.1907-0.19390.24430.07420.02410.1489-0.01380.06770.07560.02430.071651.0934-35.156420.9049
158.33041.1638-0.22051.2018-0.52130.3002-0.0435-0.2561-0.8062-0.4455-0.0801-0.49210.18220.03480.12360.38160.01430.13120.0150.03320.328953.3925-46.546118.9141
163.73710.7981-0.88132.19670.1861.5451-0.12330.2447-0.1313-0.19490.21570.32420.11-0.3896-0.09240.267-0.0283-0.0060.13570.08490.222835.2314-18.06758.3121
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 114
2X-RAY DIFFRACTION2A115 - 217
3X-RAY DIFFRACTION3A218 - 249
4X-RAY DIFFRACTION4A250 - 315
5X-RAY DIFFRACTION5B2 - 118
6X-RAY DIFFRACTION6B121 - 206
7X-RAY DIFFRACTION7B207 - 240
8X-RAY DIFFRACTION8B241 - 314
9X-RAY DIFFRACTION9C3 - 128
10X-RAY DIFFRACTION10C129 - 173
11X-RAY DIFFRACTION11C174 - 230
12X-RAY DIFFRACTION12C231 - 315
13X-RAY DIFFRACTION13D3 - 93
14X-RAY DIFFRACTION14D94 - 205
15X-RAY DIFFRACTION15D206 - 249
16X-RAY DIFFRACTION16D250 - 314

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