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- PDB-4rh6: 2.9 Angstrom Crystal Structure of Putative Exotoxin 3 from Staphy... -

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Basic information

Entry
Database: PDB / ID: 4rh6
Title2.9 Angstrom Crystal Structure of Putative Exotoxin 3 from Staphylococcus aureus.
ComponentsExotoxin 3, putative
KeywordsTOXIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / Superantigen-like protein / Exotoxin 3
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 3, putative / Exotoxin 3, putative
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMinasov, G. / Nocadello, S. / Shuvalova, L. / Filippova, E.V. / Halavaty, A. / Dubrovska, I. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. ...Minasov, G. / Nocadello, S. / Shuvalova, L. / Filippova, E.V. / Halavaty, A. / Dubrovska, I. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.9 Angstrom Crystal Structure of Putative Exotoxin 3 from Staphylococcus aureus.
Authors: Minasov, G. / Nocadello, S. / Shuvalova, L. / Filippova, E.V. / Halavaty, A. / Dubrovska, I. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural ...Authors: Minasov, G. / Nocadello, S. / Shuvalova, L. / Filippova, E.V. / Halavaty, A. / Dubrovska, I. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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: Exotoxin 3, putative
B: Exotoxin 3, putative
C: Exotoxin 3, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5906
Polymers73,4833
Non-polymers1063
Water1,874104
1
A: Exotoxin 3, putative


Theoretical massNumber of molelcules
Total (without water)24,4941
Polymers24,4941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Exotoxin 3, putative


Theoretical massNumber of molelcules
Total (without water)24,4941
Polymers24,4941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Exotoxin 3, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6014
Polymers24,4941
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.427, 90.623, 159.711
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 38 - 226 / Label seq-ID: 23 - 211

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Exotoxin 3, putative /


Mass: 24494.424 Da / Num. of mol.: 3 / Fragment: Putative Exotoxin 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Strain: COL / Gene: SACOL0468 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q5HIP9, UniProt: A0A0H2WXS6*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 8.0 mg/ml, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH(8.3); Screen: PEGs (C10), 0.1M MES (pH 6.5), 25% (w/v) PEG 8000., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 21, 2014 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 13668 / Num. obs: 13668 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 58.3 Å2 / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 10.4
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.7 / Num. unique all: 714 / Rsym value: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RDH

2rdh


Resolution: 2.9→29.96 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.88 / SU B: 39.616 / SU ML: 0.377
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R Free: 0.537 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28252 1372 10.1 %RANDOM
Rwork0.22562 ---
all0.23143 12253 --
obs0.23143 12253 95.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.042 Å2
Baniso -1Baniso -2Baniso -3
1--3.76 Å20 Å20 Å2
2---1.67 Å2-0 Å2
3---5.42 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 3 104 4695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194699
X-RAY DIFFRACTIONr_bond_other_d0.0040.024533
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.976308
X-RAY DIFFRACTIONr_angle_other_deg1.03310493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.0785571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.03125.424236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67215950
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5221524
X-RAY DIFFRACTIONr_chiral_restr0.090.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025297
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021029
X-RAY DIFFRACTIONr_mcbond_it2.523.6852281
X-RAY DIFFRACTIONr_mcbond_other2.5193.6832280
X-RAY DIFFRACTIONr_mcangle_it4.1525.5162853
X-RAY DIFFRACTIONr_mcangle_other4.1525.5182854
X-RAY DIFFRACTIONr_scbond_it2.4453.9442418
X-RAY DIFFRACTIONr_scbond_other2.4183.9442418
X-RAY DIFFRACTIONr_scangle_other4.1235.8063455
X-RAY DIFFRACTIONr_long_range_B_refined6.89728.4135219
X-RAY DIFFRACTIONr_long_range_B_other6.87528.4155204
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A10693
12B10693
21A10688
22C10688
31B10660
32C10660
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 102 -
Rwork0.319 885 -
obs--96.39 %
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)
12.7701-0.8296-0.69963.87810.47091.25870.05040.00950.1220.1238-0.04760.0528-0.01570.1071-0.00270.0290.0231-0.01070.0888-0.01840.019415.4377-10.8385-17.8796
23.2136-0.416-1.5211.959-0.39964.2377-0.2045-0.1651-0.29760.47510.12710.01040.23110.08120.07740.18690.0712-0.00170.11450.0150.031819.7122-23.9857-12.3602
32.0663-1.0131-0.60783.0057-0.72351.89960.05720.10260.18230.0887-0.0927-0.0981-0.1429-0.12280.03560.0644-0.03170.01150.0818-0.02070.0295-1.319818.8783-14.5633
44.3098-1.854-0.88236.6244-1.10273.1346-0.2613-0.01790.25220.46850.0748-0.3723-0.1870.16110.18650.2888-0.0065-0.1070.2298-0.13050.1441.138731.2567-8.8343
52.3459-0.33080.90383.24670.17962.04260.1412-0.18930.0296-0.066-0.14610.330.1396-0.11940.00490.0777-0.0396-0.00760.0512-0.01210.0395-10.473419.7381-36.0189
64.3628-0.03480.72423.3182-0.32861.5673-0.22170.01760.3017-0.1090.08980.0273-0.11720.06030.1320.03040.0001-0.00810.05790.02650.0475-0.550330.5516-39.5909
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 145
2X-RAY DIFFRACTION2A146 - 226
3X-RAY DIFFRACTION3B38 - 166
4X-RAY DIFFRACTION4B167 - 226
5X-RAY DIFFRACTION5C38 - 143
6X-RAY DIFFRACTION6C144 - 226

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