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- PDB-4zys: Crystal structure of an exotoxin 6 (SAV0422) from Staphylococcus ... -

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Basic information

Entry
Database: PDB / ID: 4zys
TitleCrystal structure of an exotoxin 6 (SAV0422) from Staphylococcus aureus subsp. aureus Mu50 at 2.25 A resolution
Componentsexotoxin 6
KeywordsSUGAR BINDING PROTEIN / exotoxin / superantigen-like protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


: / extracellular region
Similarity search - Function
Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen, staphylococcal/streptococcal toxin, bacterial / 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 / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen, staphylococcal/streptococcal toxin, bacterial / 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
Exotoxin 6 / Exotoxin=6
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an exotoxin 6 (SAV0422) from Staphylococcus aureus subsp. aureus Mu50 at 2.25 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations / Category: citation_author / pdbx_struct_oper_list
Item: _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: exotoxin 6
B: exotoxin 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9647
Polymers45,7872
Non-polymers1775
Water4,234235
1
A: exotoxin 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0004
Polymers22,8931
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: exotoxin 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9643
Polymers22,8931
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.120, 64.020, 98.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein exotoxin 6 / / Set6 protein


Mass: 22893.346 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: set6, NP_370946.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: K0L291, UniProt: A0A0M3KL42*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (31-226) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (31-226) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 30% polyethylene glycol 6000, 0.1M citric acid pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.95369,0.97937,0.97913
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 3, 2015
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953691
20.979371
30.979131
ReflectionResolution: 2.25→29.328 Å / Num. obs: 19266 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 1.921 % / Biso Wilson estimate: 31.574 Å2 / Rmerge F obs: 0.995 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.124 / Net I/σ(I): 7.14 / Num. measured all: 67264
Reflection shell
Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
2.25-2.330.7730.4851.54349361526410.661173.1
2.33-2.420.8360.4321.96013360932670.57990.5
2.42-2.530.8660.3622.27068367636390.48699
2.53-2.670.9170.2792.87422386938160.37698.6
2.67-2.830.9480.2193.76795351234770.29599
2.83-3.050.9760.1435.47201373436910.19498.8
3.05-3.360.9920.0868.27185371536810.11699.1
3.36-3.840.9960.05711.96997363835640.07798
3.84-4.830.9980.0415.97103369136160.05498
4.83-29.3280.9980.037167131374836340.05197

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XDSdata reduction
XSCALENovember 3, 2014 BUILT=20141118data scaling
SHELXDphasing
BUSTER2.10.2refinement
RefinementMethod to determine structure: MAD / Resolution: 2.25→29.328 Å / Cor.coef. Fo:Fc: 0.9509 / Cor.coef. Fo:Fc free: 0.9227 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 3. CL IONS MODELED WERE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 985 5.12 %RANDOM
Rwork0.1905 ---
obs0.193 19228 97.96 %-
Displacement parametersBiso max: 130.79 Å2 / Biso mean: 31.1552 Å2 / Biso min: 9.16 Å2
Baniso -1Baniso -2Baniso -3
1-1.4778 Å20 Å20 Å2
2--2.6059 Å20 Å2
3----4.0837 Å2
Refine analyzeLuzzati coordinate error obs: 0.273 Å
Refinement stepCycle: LAST / Resolution: 2.25→29.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 0 5 235 3366
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1587SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes106HARMONIC2
X-RAY DIFFRACTIONt_gen_planes450HARMONIC5
X-RAY DIFFRACTIONt_it3211HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion420SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3718SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3211HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4312HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion3.51
X-RAY DIFFRACTIONt_other_torsion2.94
LS refinement shellResolution: 2.25→2.37 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2441 130 5.22 %
Rwork0.2143 2361 -
all0.2159 2491 -
obs--97.96 %
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)
11.06990.3738-0.08961.56650.15760.6739-0.00920.05280.0416-0.029-0.00310.05350.01010.04090.0123-0.0882-0.0073-0.0155-0.03750.0125-0.024931.827851.398714.3034
20.7239-0.6030.07271.97930.21420.7778-0.0409-0.0836-0.01050.10870.0675-0.0357-0.0190.0653-0.0266-0.10260.00940.0145-0.02110.0211-0.019663.361950.675634.9211
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|32 - 226}A32 - 226
2X-RAY DIFFRACTION2{B|36 - 226}B36 - 226

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