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- PDB-4wxt: X-ray crystal structure of thioredoxin from Mycobacterium avium -

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Basic information

Entry
Database: PDB / ID: 4wxt
TitleX-ray crystal structure of thioredoxin from Mycobacterium avium
ComponentsThioredoxin
KeywordsHYDROLASE / infectious disease / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / thioredoxin
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 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMycobacterium avium subsp. hominissuis 3388 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: X-ray crystal structure of thioredoxin from Mycobacterium avium
Authors: Lukacs, C.M. / Arakaki, T. / Don Lorimer, D.D. / Edwards, T.E.
History
DepositionNov 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 6, 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


Theoretical massNumber of molelcules
Total (without water)13,5201
Polymers13,5201
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.070, 29.860, 31.080
Angle α, β, γ (deg.)82.64, 87.64, 66.84
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Thioredoxin


Mass: 13520.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. hominissuis 3388 (bacteria)
Gene: MAV3388_24025 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A067HWN0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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

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Sample preparation

CrystalDensity Matthews: 1.63 Å3/Da / Density % sol: 24.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: JCSG+ b2: 20% PEG 3350 0.2 M sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.87872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87872 Å / Relative weight: 1
ReflectionResolution: 1.2→5.4 Å / Num. obs: 25241 / % possible obs: 94.5 % / Redundancy: 7.8 % / Rsym value: 0.052 / Net I/σ(I): 21.8
Reflection shellResolution: 1.2→1.23 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 7.3 / % possible all: 91.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1839)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2i1u

2i1u


Resolution: 1.2→5.4 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 18.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1772 1232 4.88 %
Rwork0.1572 --
obs0.1582 25236 94.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.2→5.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms809 0 0 139 948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01850
X-RAY DIFFRACTIONf_angle_d1.3521168
X-RAY DIFFRACTIONf_dihedral_angle_d11.153310
X-RAY DIFFRACTIONf_chiral_restr0.065141
X-RAY DIFFRACTIONf_plane_restr0.008153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2001-1.24820.22541240.2012591X-RAY DIFFRACTION91
1.2482-1.3050.19741580.18772578X-RAY DIFFRACTION92
1.305-1.37380.18911350.18332596X-RAY DIFFRACTION93
1.3738-1.45990.18831660.18072604X-RAY DIFFRACTION94
1.4599-1.57260.16471240.16472691X-RAY DIFFRACTION94
1.5726-1.73080.16511360.16152705X-RAY DIFFRACTION95
1.7308-1.98130.17371180.15962723X-RAY DIFFRACTION96
1.9813-2.4960.19591390.15092744X-RAY DIFFRACTION97
2.496-30.83220.16011320.14132772X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 1.1421 Å / Origin y: -0.348 Å / Origin z: -1.5849 Å
111213212223313233
T0.0615 Å20 Å2-0.0052 Å2-0.0445 Å2-0.0052 Å2--0.0586 Å2
L1.6324 °2-0.0611 °2-0.3527 °2-0.3719 °2-0.1018 °2--1.0555 °2
S-0.0482 Å °0.0391 Å °-0.0276 Å °-0.0437 Å °0.0101 Å °0.0437 Å °-0.0217 Å °-0.0188 Å °0.0345 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 8 through 115)

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