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- PDB-4jnq: Crystal structure of a thioredoxin reductase from Brucella melitensis -

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Basic information

Entry
Database: PDB / ID: 4jnq
TitleCrystal structure of a thioredoxin reductase from Brucella melitensis
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / flavin / FAD / ebselen
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / 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
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Thioredoxin reductase
Similarity search - Component
Biological speciesBrucella melitensis bv. 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a thioredoxin reductase from Brucella melitensis
Authors: Edwards, T.E. / Arakaki, T.L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMar 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7673
Polymers36,9571
Non-polymers8112
Water4,197233
1
A: Thioredoxin reductase
hetero molecules

A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5356
Polymers73,9142
Non-polymers1,6214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557x,-y,-z+21
Buried area8150 Å2
ΔGint-66 kcal/mol
Surface area23600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.790, 77.190, 104.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Thioredoxin reductase


Mass: 36956.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis bv. 1 (bacteria) / Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BAWG_2493, BMEI0512 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8YID2, thioredoxin-disulfide reductase (NADPH)
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: BrmeA.00058.a.A1 PS01310 at 21.1 mg/mL with 2 mM ebselen against Morpheus screen condition G1: 10% PEG20000, 20% PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium ...Details: BrmeA.00058.a.A1 PS01310 at 21.1 mg/mL with 2 mM ebselen against Morpheus screen condition G1: 10% PEG20000, 20% PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate, 0.1 M MES/imidazole, pH 6.5, crystal tracking ID 241371g1, unique puck ID qoj501, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 10, 2013
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 34300 / Num. obs: 34271 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 29.839 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 24.46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.850.481418269247899.9
1.85-1.90.3725.217932244199.9
1.9-1.950.3016.5173602366100
1.95-2.010.2218.62169232292100
2.01-2.080.17710.62163632230100
2.08-2.150.14612.74160412179100
2.15-2.230.11516.05154272092100
2.23-2.320.09319.38147162002100
2.32-2.430.0822.514169192799.9
2.43-2.550.07124.65137081866100
2.55-2.680.05530.43129151763100
2.68-2.850.0534.76121601668100
2.85-3.040.04239.39115541595100
3.04-3.290.03745.25105691476100
3.29-3.60.03350.9297391376100
3.6-4.030.0355.218804125099.9
4.03-4.650.02857.737610110299.9
4.65-5.690.02657.796599958100
5.69-8.050.02456.755182766100
8.050.02355.75263644495.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å41.14 Å
Translation3 Å41.14 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CL0

1cl0


Resolution: 1.8→41.18 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1793 / WRfactor Rwork: 0.1583 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8999 / SU B: 3.879 / SU ML: 0.061 / SU R Cruickshank DPI: 0.1023 / SU Rfree: 0.0957 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1846 1728 5 %RANDOM
Rwork0.1627 ---
obs0.1639 34224 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.77 Å2 / Biso mean: 25.1871 Å2 / Biso min: 12.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å2-0 Å20 Å2
2--0.77 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 54 233 2586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192420
X-RAY DIFFRACTIONr_bond_other_d0.0010.022264
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.973313
X-RAY DIFFRACTIONr_angle_other_deg0.7683.0015178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6115319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37324.50591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72815357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.321511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022776
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02534
X-RAY DIFFRACTIONr_mcbond_it1.4451.9311264
X-RAY DIFFRACTIONr_mcbond_other1.4141.9281263
X-RAY DIFFRACTIONr_mcangle_it2.1492.8871578
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 124 -
Rwork0.236 2347 -
all-2471 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: 31.4054 Å / Origin y: 11.0268 Å / Origin z: 94.5558 Å
111213212223313233
T0.0135 Å2-0.0037 Å20.0003 Å2-0.0329 Å20.0155 Å2--0.0439 Å2
L0.0539 °20.0052 °20.0095 °2-0.0277 °20.0456 °2--0.4453 °2
S0.0055 Å °0.0057 Å °0.0426 Å °-0.0073 Å °0.0259 Å °0.0124 Å °-0.0101 Å °0.0137 Å °-0.0314 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 317
2X-RAY DIFFRACTION1A401 - 402

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