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- PDB-2nnf: Structure of the sulfur carrier protein SoxY from Chlorobium limi... -

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Basic information

Entry
Database: PDB / ID: 2nnf
TitleStructure of the sulfur carrier protein SoxY from Chlorobium limicola f thiosulfatophilum
ComponentsSulfur covalently-binding protein
KeywordsLIGAND BINDING PROTEIN / sulfur binding protein / Sox / beta sandwich / green sulfur bacterium
Function / homology
Function and homology information


SoxY domain / Sulphur oxidation, SoxY / Ig-like SoxY domain / Ig-like SoxY domain superfamily / Sulfur oxidation protein SoxY / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Sulfur covalently-binding protein
Similarity search - Component
Biological speciesChlorobium limicola (bacteria)
MethodX-RAY DIFFRACTION / Rigid Body / Resolution: 2.39 Å
AuthorsStout, J. / Van Driessche, G. / Savvides, S.N. / Van Beeumen, J.
CitationJournal: Protein Sci. / Year: 2007
Title: X-ray crystallographic analysis of the sulfur carrier protein SoxY from Chlorobium limicola f. thiosulfatophilum reveals a tetrameric structure.
Authors: Stout, J. / Van Driessche, G. / Savvides, S.N. / Van Beeumen, J.
History
DepositionOct 24, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: Sulfur covalently-binding protein
B: Sulfur covalently-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2053
Polymers26,1102
Non-polymers951
Water70339
1
A: Sulfur covalently-binding protein
B: Sulfur covalently-binding protein
hetero molecules

A: Sulfur covalently-binding protein
B: Sulfur covalently-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4116
Polymers52,2214
Non-polymers1902
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)41.220, 122.646, 97.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-126-

HOH

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Components

#1: Protein Sulfur covalently-binding protein


Mass: 13055.163 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium limicola (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q8RLX2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.4 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Ammonium phosphate, sodium phsophate, DTT, pH 4.0, vapor diffusion, hanging drop, temperature 294K

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Jan 10, 2005
RadiationMonochromator: Montel Optics (Bruker Nonius) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.39→20 Å / Num. obs: 10173 / % possible obs: 100 % / Observed criterion σ(I): 3.4 / Redundancy: 4.8 % / Rmerge(I) obs: 0.084 / Χ2: 0.97 / Net I/σ(I): 17.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.39-2.434.70.5323.44981.164100
2.43-2.484.80.5444841.09699.8
2.48-2.524.80.4615041.057100
2.52-2.574.70.4185171.126100
2.57-2.634.90.3524800.894100
2.63-2.694.80.3165010.981100
2.69-2.764.80.2635010.947100
2.76-2.834.80.234980.869100
2.83-2.924.80.1895120.957100
2.92-3.014.80.1514950.954100
3.01-3.124.80.1375090.922100
3.12-3.244.80.1125090.967100
3.24-3.394.90.0964940.995100
3.39-3.574.80.0775070.917100
3.57-3.794.80.0745220.966100
3.79-4.084.80.0695050.934100
4.08-4.484.80.0595170.954100
4.48-5.124.70.0515280.931100
5.12-6.424.70.055240.904100
6.42-204.30.0375680.87899.8

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT1.401data extraction
XPRESS(DIP2030)data collection
RefinementMethod to determine structure: Rigid Body / Resolution: 2.39→20 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 17.314 / SU ML: 0.192 / SU R Cruickshank DPI: 0.343 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.251
RfactorNum. reflection% reflectionSelection details
Rfree0.248 493 4.9 %RANDOM
Rwork0.188 ---
all0.191 ---
obs-10126 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.144 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2--0.58 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.39→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 5 39 1657
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.01116580.022
X-RAY DIFFRACTIONr_bond_other_d0.00315940.02
X-RAY DIFFRACTIONr_angle_refined_deg1.28422681.971
X-RAY DIFFRACTIONr_angle_other_deg0.72436723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9962255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.8845024
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62925015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.32815
X-RAY DIFFRACTIONr_chiral_restr0.0652830.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00418460.02
X-RAY DIFFRACTIONr_gen_planes_other0.0013090.02
X-RAY DIFFRACTIONr_nbd_refined0.1862260.2
X-RAY DIFFRACTIONr_nbd_other0.19513660.2
X-RAY DIFFRACTIONr_nbtor_refined0.1727910.2
X-RAY DIFFRACTIONr_nbtor_other0.08810050.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.091390.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.2
X-RAY DIFFRACTIONr_symmetry_vdw_other0.192290.2
X-RAY DIFFRACTIONr_mcbond_it0.56911661.5
X-RAY DIFFRACTIONr_mcbond_other0.1144501.5
X-RAY DIFFRACTIONr_mcangle_it0.7818372
X-RAY DIFFRACTIONr_scbond_it1.3925503
X-RAY DIFFRACTIONr_scangle_it2.2244314.5
LS refinement shellResolution: 2.39→2.451 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 40 -
Rwork0.236 688 -
obs--99.86 %
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)
113.54484.6924-0.265319.29629.92917.9558-0.2482-0.80640.7237-1.16140.5209-0.1271-1.29490.5506-0.2727-0.1821-0.08660.00980.07180.0414-0.305319.598960.032343.4464
23.19830.26730.55054.2424-1.06117.2465-0.11660.19440.052-0.23850.02520.2526-0.31180.41180.0913-0.2757-0.0160.0067-0.22930.0212-0.287710.237956.377134.563
314.486432.93880.840883.49082.5430.0951-0.0259-0.0673-0.85410.1731-0.071-1.65360.08790.07240.09690.0147-0.1442-0.0287-0.01970.22010.01350.583230.249352.7337
48.46422.64770.222811.3091-1.38656.1503-0.0055-0.0106-0.8446-0.5463-0.04930.45391.0548-0.29520.0548-0.123-0.0647-0.025-0.26090.0433-0.1258-1.500340.700842.6751
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA8 - 2110 - 23
22AA22 - 11724 - 119
33BB1 - 213 - 23
44BB22 - 11524 - 117

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