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- PDB-4knd: Thioredoxin from Anaeromyxobacter dehalogenans. -

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Basic information

Entry
Database: PDB / ID: 4knd
TitleThioredoxin from Anaeromyxobacter dehalogenans.
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / structural genomics / TRX_family / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Program for the Characterization of Secreted Effector Proteins / PCSEP
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 speciesAnaeromyxobacter dehalogenans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsOsipiuk, J. / Hatzos-Skintges, C. / Clancy, S. / Adkins, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Program for the Characterization of Secreted Effector Proteins (PCSEP)
CitationJournal: To be Published
Title: Thioredoxin from Anaeromyxobacter dehalogenans.
Authors: Osipiuk, J. / Hatzos-skintges, C. / Clancy, S. / Adkins, J. / Joachimiak, A.
History
DepositionMay 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)24,5342
Polymers24,5342
Non-polymers00
Water84747
1
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,2671
Polymers12,2671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,2671
Polymers12,2671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.731, 76.954, 77.208
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Detailschain A (or chain B)

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Components

#1: Protein Thioredoxin


Mass: 12266.804 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaeromyxobacter dehalogenans (bacteria)
Strain: 2CP-C / Gene: Adeh_2496 / Plasmid: pMCSG57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2IKT5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 1.96 Å3/Da / Density % sol: 37.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium chloride, 0.1 M Tris-Cl buffer, 25% PEG-3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→38.51 Å / Num. all: 15171 / Num. obs: 15171 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 52.3 Å2 / Rmerge(I) obs: 0.086 / Χ2: 3.43 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.9-1.936.10.6312.037230.65396.7
1.93-1.9770.5327630.70698.5
1.97-2.017.20.4337320.87298.8
2.01-2.057.40.3847540.92198
2.05-2.097.30.335740198
2.09-2.147.40.2857421.23598
2.14-2.197.40.2357421.2598.9
2.19-2.257.40.2117631.57998.8
2.25-2.327.30.1927441.89898.3
2.32-2.397.30.1747552.16898.7
2.39-2.487.30.1587472.53198.7
2.48-2.587.30.157642.67898.6
2.58-2.77.20.1337563.3999.2
2.7-2.847.10.1227664.20499
2.84-3.027.10.1057694.55798.8
3.02-3.2570.0967605.83499
3.25-3.586.80.0847716.65599.4
3.58-4.096.70.0747757.26299.4
4.09-5.166.70.0697917.52699
5.16-506.30.0881412.42595.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXCDphasing
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→38.51 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 10.632 / SU ML: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.168 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 754 5 %RANDOM
Rwork0.1828 ---
all0.1846 15170 --
obs0.1846 15170 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.71 Å2 / Biso mean: 52.864 Å2 / Biso min: 18.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0 Å2-0 Å2
2--4.55 Å2-0 Å2
3----4.14 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 0 47 1658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191686
X-RAY DIFFRACTIONr_bond_other_d0.0010.021696
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.9752301
X-RAY DIFFRACTIONr_angle_other_deg0.8273.0023906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2465219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.19324.70668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5415297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3871510
X-RAY DIFFRACTIONr_chiral_restr0.0930.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02346
LS refinement shellResolution: 1.904→1.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 56 -
Rwork0.307 972 -
all-1028 -
obs-1028 93.03 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9947-0.34430.57741.0062-0.08933.7359-0.1149-0.15350.0156-0.0079-0.01240.0735-0.06860.24750.12730.16680.00860.01750.06460.00220.2295-0.149341.027933.8287
21.52240.33940.26690.09710.10334.46430.16190.0815-0.0654-0.03270.0205-0.0653-0.01160.2216-0.18240.31470.02220.05110.0151-0.01510.254418.580422.503723.9312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 109
2X-RAY DIFFRACTION2B5 - 108

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