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- PDB-2xga: MTSL spin-labelled Shigella Flexneri Spa15 -

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Basic information

Entry
Database: PDB / ID: 2xga
TitleMTSL spin-labelled Shigella Flexneri Spa15
ComponentsSURFACE PRESENTATION OF ANTIGENS PROTEIN SPAK
KeywordsCHAPERONE / VIRULENCE FACTOR
Function / homologySurface presentation of antigens protein SpaK / Invasion protein B family / Yope Regulator; Chain: A, - #10 / Yope Regulator; Chain: A, / 2-Layer Sandwich / Alpha Beta / Chem-MTN / Surface presentation of antigens protein SpaK
Function and homology information
Biological speciesSHIGELLA FLEXNERI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLillington, J.E.D. / Johnson, S. / Lea, S.M.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Shigella Flexneri Spa15 Crystal Structure Verified in Solution by Double Electron Electron Resonance.
Authors: Lillington, J.E.D. / Lovett, J.E. / Johnson, S. / Roversi, P. / Timmel, C.R. / Lea, S.M.
History
DepositionJun 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1May 12, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAK
B: SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1244
Polymers34,5952
Non-polymers5292
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-9.5 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.980, 50.380, 57.680
Angle α, β, γ (deg.)90.00, 117.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.497819, -0.002596, -0.867277), (-0.019924, -0.999766, -0.008444), (-0.867052, 0.021483, -0.497754)
Vector: 29.145, 49.772, 49.621)

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Components

#1: Protein SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAK / SPA15 / CLASS 1B TYPE III SECRETION SYSTEM CHAPERONE SPA15


Mass: 17297.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MTSL SPIN LABEL BOUND TO C19 / Source: (gene. exp.) SHIGELLA FLEXNERI (bacteria) / Strain: M90T / Plasmid: PET-28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834-DE3 / References: UniProt: P35530
#2: Chemical ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL


Mass: 264.385 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18NO3S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 % / Description: NONE
Crystal growpH: 6
Details: 100 MM GUANIDINIUM CHLORIDE, 100 MM MES PH 6.0, 50 MM AMMONIUM SULPHATE, 5% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2009
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→51.38 Å / Num. obs: 19266 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 4.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0050refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RY9

1ry9


Resolution: 2.3→51.38 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.877 / SU B: 16.907 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.419 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.26375 650 5.1 %RANDOM
Rwork0.22369 ---
obs0.22574 12036 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.956 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20.53 Å2
2---1.24 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.3→51.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2038 0 24 80 2142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222116
X-RAY DIFFRACTIONr_bond_other_d0.0010.021339
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.9782889
X-RAY DIFFRACTIONr_angle_other_deg0.89633299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.995255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09525.4100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97115362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.338158
X-RAY DIFFRACTIONr_chiral_restr0.070.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022310
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02396
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0120.22116
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 51 -
Rwork0.386 869 -
obs--99.03 %
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)
14.2354-1.4331-0.25342.10120.07850.4504-0.08380.2148-0.1235-0.01690.02280.1253-0.0399-0.00810.0610.122-0.01130.00940.0935-0.00840.094235.45328.126-2.004
21.63550.6801-1.76611.209-1.75983.65140.1122-0.14870.09570.10810.01410.0699-0.05980.1935-0.12630.1192-0.0070.0050.09470.00350.144648.21420.70820.652
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 133
2X-RAY DIFFRACTION2B4 - 133

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