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- PDB-7e52: Acinetobacter baumannii Thioredoxin reductase -

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Basic information

Entry
Database: PDB / ID: 7.0E+52
TitleAcinetobacter baumannii Thioredoxin reductase
ComponentsThioredoxin reductase
KeywordsSTRUCTURAL PROTEIN / TrxR / Thioredoxin reductase / Acinetobacter baumannii
Function / homologyFAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesAcinetobacter baumannii 940793 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPark, H.H. / Chun, H.L.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Acinetobacter baumannii Thioredoxin reductase
Authors: Park, H.H. / Chun, H.L.
History
DepositionFeb 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin reductase


Theoretical massNumber of molelcules
Total (without water)34,8651
Polymers34,8651
Non-polymers00
Water61334
1
A: Thioredoxin reductase

A: Thioredoxin reductase


Theoretical massNumber of molelcules
Total (without water)69,7302
Polymers69,7302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5440 Å2
ΔGint-17 kcal/mol
Surface area25740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.100, 60.110, 73.750
Angle α, β, γ (deg.)90.000, 125.445, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Thioredoxin reductase


Mass: 34864.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii 940793 (bacteria)
Gene: trxB, J532_3818 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A062FG66, thioredoxin-disulfide reductase (NADPH)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.41 Å3/Da / Density % sol: 48.97 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 14% PEG 1000, 0.1M Tris-HCl (pH 6.4), 50mM CaCl2

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 31, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.9→26.895 Å / Num. obs: 25409 / % possible obs: 99.91 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 8.3
Reflection shellResolution: 1.9→1.949 Å / Rmerge(I) obs: 1.66 / Num. unique obs: 26880

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TRB

1trb


Resolution: 1.9→26.894 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / Cross valid method: FREE R-VALUE / ESU R: 0.167 / ESU R Free: 0.153
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2525 1271 5.004 %
Rwork0.2141 24131 -
all0.216 --
obs-25402 99.847 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.439 Å2
Baniso -1Baniso -2Baniso -3
1--0.028 Å20 Å20.014 Å2
2---0.021 Å2-0 Å2
3---0.014 Å2
Refinement stepCycle: LAST / Resolution: 1.9→26.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2349 0 0 34 2383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132389
X-RAY DIFFRACTIONr_bond_other_d0.0370.0172217
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.6313241
X-RAY DIFFRACTIONr_angle_other_deg2.361.5785094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3515312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.08423.846117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37315382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3281510
X-RAY DIFFRACTIONr_chiral_restr0.0930.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022782
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02526
X-RAY DIFFRACTIONr_nbd_refined0.2080.2382
X-RAY DIFFRACTIONr_symmetry_nbd_other0.230.21854
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21158
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21204
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1170.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2730.29
X-RAY DIFFRACTIONr_nbd_other0.2270.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0820.25
X-RAY DIFFRACTIONr_mcbond_it4.1894.0121254
X-RAY DIFFRACTIONr_mcbond_other4.1874.0081253
X-RAY DIFFRACTIONr_mcangle_it5.7795.9771564
X-RAY DIFFRACTIONr_mcangle_other5.7795.9811565
X-RAY DIFFRACTIONr_scbond_it5.474.5911135
X-RAY DIFFRACTIONr_scbond_other5.4684.5951136
X-RAY DIFFRACTIONr_scangle_it8.2336.6391677
X-RAY DIFFRACTIONr_scangle_other8.236.6421678
X-RAY DIFFRACTIONr_lrange_it9.99746.7662415
X-RAY DIFFRACTIONr_lrange_other9.99746.772415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.305930.3031772X-RAY DIFFRACTION99.9464
1.949-2.0030.33930.2871748X-RAY DIFFRACTION99.8373
2.003-2.0610.311860.2631647X-RAY DIFFRACTION100
2.061-2.1240.306870.2521641X-RAY DIFFRACTION99.8844
2.124-2.1930.257830.2451583X-RAY DIFFRACTION99.7008
2.193-2.270.276800.2381526X-RAY DIFFRACTION99.8136
2.27-2.3560.27780.2371482X-RAY DIFFRACTION99.872
2.356-2.4520.298760.2471444X-RAY DIFFRACTION99.9343
2.452-2.5610.315720.2581360X-RAY DIFFRACTION100
2.561-2.6860.27690.2451303X-RAY DIFFRACTION100
2.686-2.830.299660.2421267X-RAY DIFFRACTION100
2.83-3.0020.277620.2611171X-RAY DIFFRACTION99.919
3.002-3.2080.273580.2361111X-RAY DIFFRACTION100
3.208-3.4650.252550.221031X-RAY DIFFRACTION99.908
3.465-3.7940.27500.206947X-RAY DIFFRACTION99.501
3.794-4.240.182450.166872X-RAY DIFFRACTION99.7824
4.24-4.8920.234410.147765X-RAY DIFFRACTION99.6292
4.892-5.9810.216340.18661X-RAY DIFFRACTION100
5.981-8.4170.16270.178511X-RAY DIFFRACTION100
8.417-26.890.207160.173289X-RAY DIFFRACTION96.8254

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