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- PDB-2a87: Crystal Structure of M. tuberculosis Thioredoxin reductase -

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Basic information

Entry
Database: PDB / ID: 2a87
TitleCrystal Structure of M. tuberculosis Thioredoxin reductase
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / Thioredoxin reductase / TrxR / FAD / NAP / NMA / TLS / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


Cell redox homeostasis / thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / protein-disulfide reductase activity / NADPH binding / removal of superoxide radicals / cell redox homeostasis / flavin adenine dinucleotide binding / response to hypoxia / cytosol / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Thioredoxin reductase / Thioredoxin reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAkif, M. / Suhre, K. / Verma, C. / Mande, S.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Conformational flexibility of Mycobacterium tuberculosis thioredoxin reductase: crystal structure and normal-mode analysis.
Authors: Akif, M. / Suhre, K. / Verma, C. / Mande, S.C.
History
DepositionJul 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN FAD 348 and NAP 381 are associated with protein chain A FAD 448 and NAP 481 are ...HETEROGEN FAD 348 and NAP 381 are associated with protein chain A FAD 448 and NAP 481 are associated with protein chain B

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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)74,4748
Polymers71,3682
Non-polymers3,1076
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11050 Å2
ΔGint-44 kcal/mol
Surface area24280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.4, 107.4, 118.2
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 3

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ALAALAGLYGLYAA10 - 32210 - 322
2ARGARGHISHISBB15 - 31815 - 318
DetailsSpace group: P41212; Biological assembly is generated by the two fold axis

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Components

#1: Protein Thioredoxin reductase / / TRXR / TR


Mass: 35683.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: trxB / Plasmid: pET23(a) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P52214, UniProt: P9WHH1*PLUS, thioredoxin-disulfide reductase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.5 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 15% PEG 3350, Sodium phosphate citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.927 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 25, 2003
RadiationMonochromator: parabolic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.927 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 14186 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 89 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.083 / Net I/σ(I): 16.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 14.8 / Num. unique all: 1368 / Rsym value: 0.345 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0016refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TDE

1tde


Resolution: 3→36 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.884 / SU B: 48.839 / SU ML: 0.421 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.536 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29066 707 5 %RANDOM
Rwork0.21132 ---
obs0.21508 13357 97.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.802 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 3→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4592 0 204 16 4812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214889
X-RAY DIFFRACTIONr_bond_other_d0.0030.023182
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.996677
X-RAY DIFFRACTIONr_angle_other_deg1.0133.0037619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.215615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92122.429210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.76115716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1141553
X-RAY DIFFRACTIONr_chiral_restr0.0810.2765
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025513
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021026
X-RAY DIFFRACTIONr_nbd_refined0.2280.21219
X-RAY DIFFRACTIONr_nbd_other0.2060.23756
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22416
X-RAY DIFFRACTIONr_nbtor_other0.0850.22845
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2152
X-RAY DIFFRACTIONr_metal_ion_refined0.3470.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.23
X-RAY DIFFRACTIONr_mcbond_it2.86353860
X-RAY DIFFRACTIONr_mcbond_other0.55751278
X-RAY DIFFRACTIONr_mcangle_it4.22174843
X-RAY DIFFRACTIONr_scbond_it10.176102115
X-RAY DIFFRACTIONr_scangle_it13.589201834
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1745tight positional0.050.05
1991loose positional0.795
1745tight thermal0.080.5
1991loose thermal3.8110
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.473 68 -
Rwork0.358 945 -
obs-945 97.69 %
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)
19.3484-0.5633-0.40943.8856-0.13147.01960.11060.828-0.0708-0.63530.23311.0821-0.2423-1.7992-0.34380.1072-0.0173-0.28410.50960.35290.0848-7.1720.7635.9
25.0328-1.19092.74993.2067-0.42034.52790.1604-1.7189-1.36140.61260.66120.68471.0737-1.7566-0.8216-0.0131-0.36560.06490.23090.5377-0.1066-7.1720.7635.9
33.6061-1.1913-1.75455.50011.20379.6532-0.09430.3587-0.67570.0010.5038-0.77551.70641.6477-0.40960.2002-0.06690.1304-0.2083-0.19470.132422.5226.3110.18
43.5341-0.77810.60454.19290.14884.65740.12270.9684-0.0117-1.17230.2064-0.95720.16291.1041-0.32910.0006-0.08640.2467-0.1315-0.219-0.135222.5226.3110.18
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA126 - 250126 - 250
2X-RAY DIFFRACTION2AA10 - 12510 - 125
3X-RAY DIFFRACTION2AA251 - 322251 - 322
4X-RAY DIFFRACTION3BB126 - 250126 - 250
5X-RAY DIFFRACTION4BB15 - 12515 - 125
6X-RAY DIFFRACTION4BB251 - 318251 - 318

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