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- PDB-3dml: Crystal structure of the periplasmic thioredoxin SoxS from Paraco... -

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Basic information

Entry
Database: PDB / ID: 3dml
TitleCrystal structure of the periplasmic thioredoxin SoxS from Paracoccus pantotrophus (reduced form)
ComponentsPutative uncharacterized protein
KeywordsOXIDOREDUCTASE / thioredoxin / sulfur oxidation / thiol-disulfide oxidoreductase
Function / homologyThioredoxin-like domain / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta / Thioredoxin-like fold domain-containing protein
Function and homology information
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsCarius, Y. / Friedrich, C.G. / Scheidig, A.J.
CitationJournal: To be Published
Title: Crystal structure of the periplasmic thioredoxin SoxS from Paracoccus pantotrophus indicates a dual Trx/Grx functionality for activation of chemotrophic sulfur oxidation in vivo
Authors: Carius, Y. / Rother, D. / Friedrich, C.G. / Scheidig, A.J.
History
DepositionJul 1, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)13,3151
Polymers13,3151
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.909, 80.909, 33.212
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

21A-515-

HOH

31A-603-

HOH

41A-655-

HOH

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Components

#1: Protein Putative uncharacterized protein / Thiol-disulfide oxidoreductase SoxS


Mass: 13315.221 Da / Num. of mol.: 1 / Fragment: periplasmic domain, UNP residues 32-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: GB17 / Gene: soxS / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4]
References: UniProt: Q8KM22, Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1M citrate, 0.4M sodium phosphate, 0.4M potassium phosphate, 3% (w/v) glucose, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.95369, 0.97833, 0.97838, 1.0332
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 22, 2006 / Details: mirrors
RadiationMonochromator: Double crystal Si[111] / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953691
20.978331
30.978381
41.03321
ReflectionResolution: 1.9→20.71 Å / Num. all: 10064 / Num. obs: 9998 / % possible obs: 99.3 % / Redundancy: 6.3 % / Biso Wilson estimate: 18.37 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 30.87
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 6.36 / Num. unique all: 662 / Rsym value: 0.447 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345CCDdata collection
DENZOdata reduction
SCALEPACKdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→20.71 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.867 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20124 480 4.8 %RANDOM
Rwork0.1544 ---
all0.15668 9557 --
obs0.15668 9530 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.168 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å20 Å2
3----0.45 Å2
Refine analyzeLuzzati coordinate error free: 0.124 Å
Refinement stepCycle: LAST / Resolution: 1.9→20.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms799 0 0 162 961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022829
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5122.0041141
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6675110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72323.17141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95415138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.553159
X-RAY DIFFRACTIONr_chiral_restr0.0980.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02668
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.2400
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.2553
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2114
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6591.5520
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7382818
X-RAY DIFFRACTIONr_scbond_it2.8473358
X-RAY DIFFRACTIONr_scangle_it4.1574.5315
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 32 -
Rwork0.199 684 -
obs-684 97.28 %

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