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

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Basic information

Entry
Database: PDB / ID: 2nnc
TitleStructure of the sulfur carrier protein SoxY from Chlorobium limicola f thiosulfatophilum
ComponentsSulfur covalently-binding protein
KeywordsLIGAND BINDING PROTEIN / sulfur binding protein / SoxY / 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
NITROGEN MOLECULE / PHOSPHATE ION / Sulfur covalently-binding protein
Similarity search - Component
Biological speciesChlorobium limicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / MIRAS / Resolution: 2.14 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 / Item: _software.name
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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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
A: Sulfur covalently-binding protein
B: Sulfur covalently-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3257
Polymers26,1102
Non-polymers2145
Water84747
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)52,65014
Polymers52,2214
Non-polymers42910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)40.725, 120.114, 95.303
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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) / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: Q8RLX2
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-HDZ / NITROGEN MOLECULE


Mass: 28.013 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2342.8
22.4147
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Ammonium phosphate, sodium acetate, DTT, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
22931
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG BW7A11.06
SYNCHROTRONEMBL/DESY, HAMBURG BW7A21.04
Detector
TypeIDDetectorDate
MARRESEARCH1CCDFeb 2, 2005
MARRESEARCH2CCDMay 26, 2005
Radiation
IDProtocolScattering typeWavelength-ID
1SINGLE WAVELENGTHx-ray1
2SINGLE WAVELENGTHx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.061
21.041
ReflectionResolution: 2.14→99 Å / Num. obs: 13122 / % possible obs: 98.1 % / Observed criterion σ(I): 5.6 / Redundancy: 7.81 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 33.4
Reflection shellResolution: 2.14→2.2 Å / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 5.6 / Num. unique all: 831 / % possible all: 97.8

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Phasing

PhasingMethod: MIRAS
Phasing MIRResolution: 3→25 Å / FOM: 0.49 / Reflection: 4946
Phasing MIR shell
Resolution (Å)FOMReflection
10.28-250.66275
6.67-10.280.66428
5.27-6.670.61533
4.49-5.270.51606
3.97-4.490.49680
3.6-3.970.43749
3.32-3.60.4815
3.1-3.320.37860

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Processing

Software
NameVersionClassificationNB
SOLVE2.08phasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACT1.401data extraction
MAR345345DTBdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.14→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.934 / SU B: 14.828 / SU ML: 0.189 / SU R Cruickshank DPI: 0.272 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.213 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 619 4.9 %RANDOM
Rwork0.216 ---
all0.218 ---
obs-12527 94.38 %-
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: 45.075 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20 Å20 Å2
2--1.14 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.14→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 12 47 1672
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.01116480.022
X-RAY DIFFRACTIONr_bond_other_d0.00115760.02
X-RAY DIFFRACTIONr_angle_refined_deg1.31722481.975
X-RAY DIFFRACTIONr_angle_other_deg0.71736373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3642235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.4154824.792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33825315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.826615
X-RAY DIFFRACTIONr_chiral_restr0.0692820.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00418190.02
X-RAY DIFFRACTIONr_gen_planes_other0.0012940.02
X-RAY DIFFRACTIONr_nbd_refined0.1792760.2
X-RAY DIFFRACTIONr_nbd_other0.19214540.2
X-RAY DIFFRACTIONr_nbtor_refined0.1717890.2
X-RAY DIFFRACTIONr_nbtor_other0.0869870.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.138450.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.13100.2
X-RAY DIFFRACTIONr_symmetry_vdw_other0.189430.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.03910.2
X-RAY DIFFRACTIONr_mcbond_it0.57111651.5
X-RAY DIFFRACTIONr_mcbond_other0.1184481.5
X-RAY DIFFRACTIONr_mcangle_it0.78818262
X-RAY DIFFRACTIONr_scbond_it1.3545463
X-RAY DIFFRACTIONr_scangle_it2.1554224.5
LS refinement shellResolution: 2.141→2.196 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 16 -
Rwork0.257 302 -
obs--33.09 %
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)
16.70438.8574-5.335227.99731.126811.29640.0715-0.23150.3573-0.64770.30790.1431-1.06310.8711-0.3794-0.2222-0.0953-0.01270.19250.1118-0.272518.97958.747842.5442
24.1433-0.71291.22133.9572-1.12678.0375-0.12170.0251-0.1295-0.2012-0.04320.1983-0.32410.5920.165-0.2153-0.07150.0238-0.22620.0426-0.29069.964955.519633.7477
35.082915.4043-1.945855.1183-5.19050.8040.1257-0.5823-0.95350.386-0.7671-1.811-0.12130.47440.6414-0.0452-0.168-0.11030.16750.54810.4030.334929.42651.4867
48.76543.9141.09610.9809-1.9035.31440.1911-0.2035-1.0289-0.607-0.06580.320.9538-0.2838-0.1253-0.0793-0.102-0.0493-0.18390.14460.0164-1.925639.750141.5862
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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