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- PDB-6ckp: Crystal structure of a thioredoxin domain 2 from Brucella meliten... -

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Basic information

Entry
Database: PDB / ID: 6ckp
TitleCrystal structure of a thioredoxin domain 2 from Brucella melitensis at 1.15 Angstrom resolution
ComponentsThioredoxin
KeywordsELECTRON TRANSPORT / SSGCID / Brucella melitensis / Thioredoxin / domain-2 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glycerol ether metabolic process / protein-disulfide reductase activity / cell redox homeostasis
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 speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a thioredoxin domain 2 from Brucella melitensis at 1.15 Angstrom resolution
Authors: Mayclin, S.J. / Dranow, D.M. / Buchko, G.W. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionFeb 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)13,7201
Polymers13,7201
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.240, 40.240, 63.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Thioredoxin


Mass: 13719.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: abortus 2308 / Gene: BK187_10725 / Plasmid: BrabA.00029.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Z1ZP61, UniProt: Q2YQX0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 1.89 Å3/Da / Density % sol: 34.8 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.4 mg/mL BrabA.00029.a.A1.PB00087 with Emerald Biostructures Primary Precipitant #18 (2 M lithium sulfate, 2% PEG400, 100 mM Tris base, pH 8.5), dc, lbx1-3

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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: Feb 8, 2018
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 36050 / % possible obs: 100 % / Redundancy: 6.07 % / Biso Wilson estimate: 11.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.06 / Χ2: 1.023 / Net I/σ(I): 15.15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.15-1.185.9560.5692.7826620.8230.625100
1.18-1.215.9680.4873.3225770.8760.533100
1.21-1.255.9830.4034.0825220.910.442100
1.25-1.296.0070.3394.8424430.9320.371100
1.29-1.336.0390.2785.8723860.9580.304100
1.33-1.376.0850.2287.122830.970.249100
1.37-1.436.1310.1928.4722360.9780.21100
1.43-1.486.1410.14411.121370.9870.158100
1.48-1.556.0790.11613.9320600.9920.12799.9
1.55-1.636.1730.09416.3819280.9940.103100
1.63-1.716.2230.08119.318700.9950.088100
1.71-1.826.1870.06722.8317630.9960.074100
1.82-1.946.1660.05626.4816510.9980.061100
1.94-2.16.0670.0529.9715510.9980.055100
2.1-2.36.0570.04532.2214250.9980.05100
2.3-2.576.0730.04133.5212820.9990.04599.9
2.57-2.976.1180.0435.4411400.9990.04399.9
2.97-3.646.0140.03836.719620.9990.04299.9
3.64-5.146.0150.03537.547530.9980.038100
5.14-40.245.8160.03636.824190.9970.0499.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
Coot3.24model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2YJ7

2yj7


Resolution: 1.15→50 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 14.66
RfactorNum. reflection% reflection
Rfree0.1612 2096 5.81 %
Rwork0.1405 --
obs0.1417 36050 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.84 Å2 / Biso mean: 16.6848 Å2 / Biso min: 7.41 Å2
Refinement stepCycle: final / Resolution: 1.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms875 0 0 163 1038
Biso mean---27.98 -
Num. residues----119
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.15-1.17680.20261460.18162248
1.1768-1.20620.20231230.16552261
1.2062-1.23880.19261220.15532294
1.2388-1.27530.19371210.14932240
1.2753-1.31640.15971290.14222294
1.3164-1.36350.1721470.13012232
1.3635-1.41810.15561560.12352243
1.4181-1.48260.13381660.11462256
1.4826-1.56080.15881150.1162259
1.5608-1.65860.15851680.11972226
1.6586-1.78670.1521890.12422224
1.7867-1.96640.1491300.12772283
1.9664-2.2510.13491250.12892297
2.251-2.83590.1721370.1582278
2.8359-500.16731220.15052319

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