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- PDB-7xao: Crystal structure of thioredoxin 1 -

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Basic information

Entry
Database: PDB / ID: 7xao
TitleCrystal structure of thioredoxin 1
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / Trx1 / thioredoxin1
Function / homology
Function and homology information


protein-disulfide reductase activity / cell redox homeostasis / cytosol
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsChang, Y.J. / Park, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: High-resolution crystal structure of Acinetobacter baumannii thioredoxin 1.
Authors: Chang, Y.J. / Park, H.H.
History
DepositionMar 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)23,2142
Polymers23,2142
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-8 kcal/mol
Surface area10140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.240, 31.270, 215.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Thioredoxin


Mass: 11607.187 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: trxA, trx / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V5VGM8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: 0.1M SPG buffer/NaOH pH 5.7, 23% PEG 1500

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Data collection

DiffractionMean temperature: 125 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→28.68 Å / Num. obs: 38852 / % possible obs: 99.8 % / Redundancy: 12.7 % / Biso Wilson estimate: 15.51 Å2 / Rmerge(I) obs: 0.09338 / Net I/σ(I): 17.59
Reflection shellResolution: 1.45→1.45 Å / Rmerge(I) obs: 0.4213 / Num. unique obs: 3820

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
PHENIX1.17_3644refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2yn1

2yn1


Resolution: 1.45→28.68 Å / SU ML: 0.2026 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.3678
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2833 1994 5.14 %
Rwork0.2456 36808 -
obs0.2475 38802 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.78 Å2
Refinement stepCycle: LAST / Resolution: 1.45→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1606 0 0 201 1807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591634
X-RAY DIFFRACTIONf_angle_d0.83742234
X-RAY DIFFRACTIONf_chiral_restr0.0827274
X-RAY DIFFRACTIONf_plane_restr0.0055286
X-RAY DIFFRACTIONf_dihedral_angle_d4.9469216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.31311410.27842622X-RAY DIFFRACTION98.82
1.49-1.530.31441310.26552496X-RAY DIFFRACTION99.39
1.53-1.570.30541450.25972610X-RAY DIFFRACTION99.71
1.57-1.620.29791390.26062549X-RAY DIFFRACTION99.85
1.62-1.680.29251390.25542586X-RAY DIFFRACTION99.82
1.68-1.750.32661390.25872627X-RAY DIFFRACTION99.96
1.75-1.830.29921440.24682595X-RAY DIFFRACTION99.96
1.83-1.920.27531410.24942582X-RAY DIFFRACTION100
1.92-2.040.28521410.24842614X-RAY DIFFRACTION99.96
2.04-2.20.25441470.24642642X-RAY DIFFRACTION99.96
2.2-2.420.28671410.25042659X-RAY DIFFRACTION99.96
2.42-2.770.31411420.25982646X-RAY DIFFRACTION100
2.77-3.490.26671490.24312730X-RAY DIFFRACTION100
3.49-28.680.2691550.22362850X-RAY DIFFRACTION99.97

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