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- PDB-3qdn: Putative thioredoxin protein from Salmonella typhimurium -

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Basic information

Entry
Database: PDB / ID: 3qdn
TitlePutative thioredoxin protein from Salmonella typhimurium
ComponentsPutative thioredoxin protein
KeywordsOXIDOREDUCTASE / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / ybbN
Function / homology
Function and homology information


Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Glutaredoxin / Glutaredoxin / Alpha Horseshoe ...Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Thioredoxin / Thioredoxin domain profile. / Thioredoxin domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Glutaredoxin / Glutaredoxin / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Putative thioredoxin protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsOsipiuk, J. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Putative thioredoxin protein from Salmonella typhimurium.
Authors: Osipiuk, J. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionJan 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative thioredoxin protein
B: Putative thioredoxin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7704
Polymers64,6892
Non-polymers802
Water1,69394
1
A: Putative thioredoxin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4253
Polymers32,3451
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative thioredoxin protein


Theoretical massNumber of molelcules
Total (without water)32,3451
Polymers32,3451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.234, 62.547, 79.522
Angle α, β, γ (deg.)90.00, 98.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative thioredoxin protein /


Mass: 32344.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: STM0504, ybbN / Plasmid: pMCSG7 / Culture collection (production host): 469008 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZR92
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG-3000, 0.2 M calcium acetate, 0.1 M Tris buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 10, 2009
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: 2.12→35.7 Å / Num. all: 32295 / Num. obs: 32295 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 10
Reflection shellResolution: 2.12→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 1.77 / Num. unique all: 1571 / % possible all: 96.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.09→35.7 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 18.794 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.33 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30189 1625 5 %RANDOM
Rwork0.24174 ---
all0.24486 30611 --
obs0.24486 30611 96.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å2-0.16 Å2
2---0.22 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.09→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4447 0 2 94 4543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224709
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5781.9726430
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.095617
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.84726.31252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.14715866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.071525
X-RAY DIFFRACTIONr_chiral_restr0.1010.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213641
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8191.52909
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.53224690
X-RAY DIFFRACTIONr_scbond_it2.31131800
X-RAY DIFFRACTIONr_scangle_it3.8824.51711
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.094→2.148 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 73 -
Rwork0.334 1357 -
obs-1430 57.94 %
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)
10.2035-0.17870.19740.3793-0.14130.20540.01520.0649-0.028-0.01940.0083-0.03550.00880.0537-0.02350.0570.00640.03120.1041-0.00060.075460.05722.556261.0833
20.63290.17630.4950.07560.20170.5865-0.11710.22870.1389-0.03250.01650.0322-0.12250.12260.10050.223-0.022-0.00670.23240.0320.253689.00421.147161.0516
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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