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- PDB-4o1n: Crystal structure of Staphylococcal superantigen-like protein SAO... -

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Basic information

Entry
Database: PDB / ID: 4o1n
TitleCrystal structure of Staphylococcal superantigen-like protein SAOUHSC_00383
ComponentsSuperantigen-like protein
KeywordsSUGAR BINDING PROTEIN / oligosaccharide-binding / beta-grasp domain
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / peptidase activity / proteolysis / extracellular region
Similarity search - Function
Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin ...Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Staphylococcal superantigen-like 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsDutta, D. / Dutta, A. / Basak, A. / Das, A.K.
CitationJournal: To be Published
Title: Crystal structure of Staphylococcal superantigen-like protein SAOUHSC_00383
Authors: Dutta, D. / Dutta, A. / Basak, A. / Das, A.K.
History
DepositionDec 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
A: Superantigen-like protein
B: Superantigen-like protein
C: Superantigen-like protein
D: Superantigen-like protein
E: Superantigen-like protein
F: Superantigen-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,9699
Polymers145,6936
Non-polymers2763
Water2,756153
1
A: Superantigen-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3742
Polymers24,2821
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Superantigen-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3742
Polymers24,2821
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Superantigen-like protein


Theoretical massNumber of molelcules
Total (without water)24,2821
Polymers24,2821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Superantigen-like protein


Theoretical massNumber of molelcules
Total (without water)24,2821
Polymers24,2821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Superantigen-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3742
Polymers24,2821
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Superantigen-like protein


Theoretical massNumber of molelcules
Total (without water)24,2821
Polymers24,2821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.900, 70.500, 126.500
Angle α, β, γ (deg.)90.000, 106.200, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERVALVALAA14 - 4723 - 56
21SERSERVALVALBB14 - 4723 - 56
12SERSERSERSERAA54 - 10063 - 109
22SERSERSERSERBB54 - 10063 - 109
13PROPROHISHISAA110 - 150119 - 159
23PROPROHISHISBB110 - 150119 - 159
14LEULEUASNASNAA152 - 155161 - 164
24LEULEUASNASNBB152 - 155161 - 164
15LEULEUMETMETAA157 - 201166 - 210
25LEULEUMETMETBB157 - 201166 - 210
DetailsAUTHOR STATED THE FUNCTION OF THE PROTEIN WAS NOT CLARIFIED, THEREFOR THE BIOLOGICAL ASSEMBLY WAS ALSO DIFFICULT TO PREDICT. GEL FILTRATION INDICATED TRIMER.

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Components

#1: Protein
Superantigen-like protein


Mass: 24282.180 Da / Num. of mol.: 6 / Fragment: UNP residues 26-226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: NCTC 8325 / Gene: SAOUHSC_00383 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q2G0X9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.29 Å3/Da / Density % sol: 46.28 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 6% TACSIMATE pH 6.0, 25% (W/V) PEG 3350 , 0.1M MES pH 6.0, 0.1M NDSB-256, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 9, 2013 / Details: MIRRORS
RadiationMonochromator: VARIMAX (OSMIC MIRROR) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→121.477 Å / Num. all: 45615 / Num. obs: 45615 / % possible obs: 99.4 % / Redundancy: 4.3 % / Rsym value: 0.061 / Net I/σ(I): 20.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.5-2.634.30.4490.39322825265610.2150.4490.3933.998.7
2.63-2.794.30.3170.2782.82700862690.1510.3170.2785.499.4
2.79-2.994.30.2160.1894.12544558780.1030.2160.1897.899.3
2.99-3.234.30.1330.1176.72384555120.0630.1330.11712.199.7
3.23-3.544.30.0770.06811.52215851120.0370.0770.06820.499.9
3.54-3.954.30.0490.04317.91995645970.0230.0490.04329.7100
3.95-4.564.30.0340.0324.51775540830.0160.0340.0339.8100
4.56-5.594.30.030.026271510234780.0140.030.02645.4100
5.59-7.94.30.0330.02924.71166327020.0150.0330.02938.7100
7.9-19.6784.20.0190.01638.3598914230.0090.0190.01663.193.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RDG

2rdg


Resolution: 2.5→19.69 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.887 / WRfactor Rfree: 0.2388 / WRfactor Rwork: 0.1737 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7825 / SU B: 24.565 / SU ML: 0.262 / SU R Cruickshank DPI: 0.6257 / SU Rfree: 0.3333 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.626 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2835 2300 5 %RANDOM
Rwork0.2052 ---
obs0.2091 45608 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.78 Å2 / Biso mean: 45.573 Å2 / Biso min: 12.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å2-0 Å22.65 Å2
2---3.62 Å2-0 Å2
3---2.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9046 0 18 153 9217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0199183
X-RAY DIFFRACTIONr_bond_other_d0.0010.028757
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.96812327
X-RAY DIFFRACTIONr_angle_other_deg0.844320215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.88851130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48825.248444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.697151781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8261546
X-RAY DIFFRACTIONr_chiral_restr0.0940.21371
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210349
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022010
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1672MEDIUM POSITIONAL0.040.5
1012TIGHT THERMAL5.920.5
1672MEDIUM THERMAL6.972
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 171 -
Rwork0.313 3127 -
all-3298 -
obs--98.8 %
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)
10.3484-0.1494-0.4550.596-0.03360.74490.0250.0479-0.0402-0.0875-0.030.1158-0.0213-0.0330.00510.02370.0059-0.01410.0908-0.00870.0263-30.197223.665155.4893
20.2412-0.1905-0.22970.64960.12380.4992-0.00540.0527-0.0921-0.0923-0.01580.0281-0.0531-0.02890.02120.03970.00420.02460.1006-0.05040.0633-8.2912-4.9132.4354
30.58220.048-0.42350.7189-0.260.4212-0.0146-0.0182-0.030.1110.0172-0.0502-0.04970.0254-0.00260.0330.00160.01750.0731-0.00130.0437-32.9817-35.293212.2811
40.5738-0.0541-0.25180.5955-0.10250.32040.0014-0.0347-0.02750.05150.0409-0.1324-0.11180.0581-0.04240.081-0.06290.04050.088-0.03890.0786-11.1102-7.3144-10.8002
51.30730.631-0.43540.5588-0.2980.5145-0.0527-0.0022-0.03430.0361-0.0265-0.02860.0740.02150.07920.05780.02870.04020.05160.04010.0454-49.40310.397728.9425
60.50940.3419-0.11230.5598-0.38621.05870.1096-0.04870.06190.0064-0.0605-0.1024-0.0217-0.0382-0.04910.052-0.01890.06620.05750.00270.1186-67.427323.306148.4881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 202
2X-RAY DIFFRACTION2B14 - 202
3X-RAY DIFFRACTION3C14 - 202
4X-RAY DIFFRACTION4D13 - 202
5X-RAY DIFFRACTION5E14 - 202
6X-RAY DIFFRACTION6F13 - 202

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