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- PDB-2ox5: The SoxYZ complex of Paracoccus pantotrophus -

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Basic information

Entry
Database: PDB / ID: 2ox5
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
ACETATE ION / SoxZ protein / SoxY protein
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.98 Å
AuthorsBruno, S. / Sauve, 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 19, 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 1.3Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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)93,69320
Polymers92,8708
Non-polymers82312
Water16,123895
1
Z: SoxZ protein
Y: SoxY protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4325
Polymers23,2182
Non-polymers2143
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-15 kcal/mol
Surface area10410 Å2
MethodPISA
2
A: SoxZ protein
B: SoxY protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7059
Polymers23,2182
Non-polymers4877
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-32 kcal/mol
Surface area10210 Å2
MethodPISA
3
C: SoxZ protein
D: SoxY protein


Theoretical massNumber of molelcules
Total (without water)23,2182
Polymers23,2182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-6 kcal/mol
Surface area9910 Å2
MethodPISA
4
E: SoxZ protein
F: SoxY protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3394
Polymers23,2182
Non-polymers1212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-9 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.605, 54.708, 77.884
Angle α, β, γ (deg.)90.00, 98.58, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a SoxYZ heterodimer. The crystallographic asymmetric unit contains two copies of this biological assembly.

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Components

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Protein , 2 types, 8 molecules ZACEYBDF

#1: Protein
SoxZ protein


Mass: 11781.041 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 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9LCU8
#2: Protein
SoxY protein


Mass: 11436.581 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 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9LCU9

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Non-polymers , 4 types, 907 molecules

#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 895 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.34 Å3/Da / Density % sol: 47.48 %
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 8.0, 5 mM beta-mercaptoethanol and 200 mM NaCl mixed with 2 microl of 28-30 % (w/v) PEG 3350, 100 mM sodium acetate pH 4.75, 200 mM ...Details: 2 microl of protein at 10 mg/ml in 10 mM Tris-HCl pH 8.0, 5 mM beta-mercaptoethanol and 200 mM NaCl mixed with 2 microl of 28-30 % (w/v) PEG 3350, 100 mM sodium acetate pH 4.75, 200 mM NH4SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9793, 0.8731
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 3, 2003
RadiationMonochromator: Si(111) monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.87311
ReflectionResolution: 1.981→102.147 Å / Num. all: 59443 / Num. obs: 59443 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.98-2.0930.272.72348778760.2791.3
2.09-2.214.20.2083.63452082760.208100
2.21-2.374.20.1614.53253578140.161100
2.37-2.564.20.1285.73031072490.128100
2.56-2.84.20.0967.62808167000.096100
2.8-3.134.20.0710.22537660530.07100
3.13-3.614.20.04613.72252853520.046100
3.61-4.434.20.03915.21908345500.039100
4.43-6.264.10.03913.71465635670.039100
6.26-39.913.90.04411.5786820060.04499.6

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
MOSFLMdata reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.98→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.416 / SU ML: 0.099 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 3006 5.1 %RANDOM
Rwork0.173 ---
all0.175 59443 --
obs0.175 59443 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.604 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20.31 Å2
2--0.74 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6335 0 51 895 7281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226473
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9728801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3535866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3125.56241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18215997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8231527
X-RAY DIFFRACTIONr_chiral_restr0.0960.21051
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024853
X-RAY DIFFRACTIONr_nbd_refined0.2040.23017
X-RAY DIFFRACTIONr_nbtor_refined0.2990.24386
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2751
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.251
X-RAY DIFFRACTIONr_mcbond_it0.8381.54459
X-RAY DIFFRACTIONr_mcangle_it1.3426958
X-RAY DIFFRACTIONr_scbond_it2.22932228
X-RAY DIFFRACTIONr_scangle_it3.5384.51840
LS refinement shellResolution: 1.981→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 210 -
Rwork0.203 3443 -
obs-3653 82.72 %

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