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- PDB-2oxg: The SoxYZ Complex of Paracoccus pantotrophus -

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Basic information

Entry
Database: PDB / ID: 2oxg
TitleThe SoxYZ Complex of Paracoccus pantotrophus
Components
  • SoxY protein
  • SoxZ protein
KeywordsTRANSPORT PROTEIN / immunoglobulin-like beta-sandwich fold
Function / homology
Function and homology information


Sulphur oxidation protein SoxZ / Thiosulfate oxidation carrier complex protein SoxZ / Sulphur oxidation protein SoxZ / SoxY domain / Sulphur oxidation, SoxY / Ig-like SoxY domain / Ig-like SoxY domain superfamily / Sulfur oxidation protein SoxY / Immunoglobulin E-set / Immunoglobulin-like fold ...Sulphur oxidation protein SoxZ / Thiosulfate oxidation carrier complex protein SoxZ / Sulphur oxidation protein SoxZ / SoxY domain / Sulphur oxidation, SoxY / Ig-like SoxY domain / Ig-like SoxY domain superfamily / Sulfur oxidation protein SoxY / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
SoxZ protein / SoxY protein
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSauve, V. / Berks, B.C. / Hemmings, A.M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The SoxYZ Complex Carries Sulfur Cycle Intermediates on a Peptide Swinging Arm.
Authors: Sauve, V. / Bruno, S. / Berks, B.C. / Hemmings, A.M.
History
DepositionFeb 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Z: SoxZ protein
Y: SoxY protein
A: SoxZ protein
B: SoxY protein
C: SoxZ protein
D: SoxY protein
E: SoxZ protein
F: SoxY protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,03315
Polymers96,4968
Non-polymers5367
Water13,583754
1
Z: SoxZ protein
Y: SoxY protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2824
Polymers24,1242
Non-polymers1582
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-13 kcal/mol
Surface area10250 Å2
MethodPISA
2
A: SoxZ protein
B: SoxY protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3445
Polymers24,1242
Non-polymers2203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-19 kcal/mol
Surface area9770 Å2
MethodPISA
3
C: SoxZ protein
D: SoxY protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2203
Polymers24,1242
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-3 kcal/mol
Surface area9610 Å2
MethodPISA
4
E: SoxZ protein
F: SoxY protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1863
Polymers24,1242
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-3 kcal/mol
Surface area9590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.828, 54.717, 77.677
Angle α, β, γ (deg.)90.00, 98.68, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is the SoxYZ heterodimer. The crystallographic asymmetric unit contains 4 copies of the biological unit.

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Components

#1: Protein
SoxZ protein


Mass: 11734.146 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: LMD82.5T / Gene: soxZ / Plasmid: PVS005 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9LCU8
#2: Protein
SoxY protein


Mass: 12389.928 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: LMD82.5T / Gene: soxY / Plasmid: PVS005 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9LCU9
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 754 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2 microl of protein at 10 mg/ml in 10 mM Tris-HCl pH 8, 5 mM DTT and 2 microl of 31-32 % (w/v) PEG 3350, 100 mM sodium acetate pH 4.75, 200 mM NH4SO4 and 2 % (v/v) glycerol, pH 8.0, VAPOR ...Details: 2 microl of protein at 10 mg/ml in 10 mM Tris-HCl pH 8, 5 mM DTT and 2 microl of 31-32 % (w/v) PEG 3350, 100 mM sodium acetate pH 4.75, 200 mM NH4SO4 and 2 % (v/v) glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 17, 2003 / Details: Diamond (111), Laue geometry, 150 microns thin
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.4→102.229 Å / Num. all: 164928 / Num. obs: 164928 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 7.6
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 1.7 / Num. measured all: 44294 / Num. unique all: 23687 / Rsym value: 0.395 / % possible all: 96.7

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OX5

2ox5


Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.954 / SU ML: 0.035 / Isotropic thermal model: ANISOTROPIC INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 8301 5 %RANDOM
Rwork0.168 ---
all0.17 164923 --
obs0.17 164923 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.941 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.15 Å2
2--0.24 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6309 0 31 754 7094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226451
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9658823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2595891
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80125.57237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81715978
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4881526
X-RAY DIFFRACTIONr_chiral_restr0.0920.21066
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024880
X-RAY DIFFRACTIONr_nbd_refined0.2090.22917
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24502
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2621
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.236
X-RAY DIFFRACTIONr_mcbond_it1.5131.54467
X-RAY DIFFRACTIONr_mcangle_it2.20227016
X-RAY DIFFRACTIONr_scbond_it3.23632201
X-RAY DIFFRACTIONr_scangle_it4.6524.51794
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 604 -
Rwork0.253 11250 -
obs-11854 95.36 %

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