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- PDB-4a4y: Structure of the Cytosolic Domain of the Shigella T3SS component MxiG -

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Basic information

Entry
Database: PDB / ID: 4a4y
TitleStructure of the Cytosolic Domain of the Shigella T3SS component MxiG
ComponentsPROTEIN MXIG
KeywordsPROTEIN BINDING / FHA DOMAIN
Function / homologyTumour Suppressor Smad4 - #50 / Type III secretion system, PrgH/EprH-like / Type III secretion system protein PrgH-EprH (PrgH) / Tumour Suppressor Smad4 / cell outer membrane / Sandwich / Mainly Beta / plasma membrane / Protein MxiG
Function and homology information
Biological speciesSHIGELLA FLEXNERI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsBarison, N. / Kolbe, M.
CitationJournal: Faseb J. / Year: 2012
Title: Interaction of Mxig with the Cytosolic Complex of the Type III Secretion System Controls Shigella Virulence.
Authors: Barison, N. / Lambers, J. / Hurwitz, R. / Kolbe, M.
History
DepositionOct 20, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Other
Revision 1.2Apr 11, 2012Group: Other
Revision 1.3Apr 25, 2012Group: Other
Revision 1.4May 1, 2024Group: Data collection / Database references ...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 / 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_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: PROTEIN MXIG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6843
Polymers16,4991
Non-polymers1842
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.790, 94.790, 31.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PROTEIN MXIG


Mass: 16499.324 Da / Num. of mol.: 1 / Fragment: CYTOPLASMIC DOMAIN, RESIDUES 1-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SHIGELLA FLEXNERI (bacteria) / Strain: M90T / Variant: SEROTYPE 5A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A221
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL HIS-TAG

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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: 2.83 Å3/Da / Density % sol: 56.57 %
Description: SE-MET STRUCTURE SOLVED USING SOLVE-RESOLVE ANALYSIS OF 4 WAVELENGTH MAD: PEAK 0.97962 A, INFLECTION 0.97973 A, REMOTE (HIGH E) 0.97194 A, REMOTE (LOW E) 0.99535 A.
Crystal growDetails: PROTEIN WAS CRYSTALLIZED FROM 0.085 M HEPES SODIUM PH 7.5, 1.7% POLYETHYLENE GLYCOL 400, 1.7 M AMMONIUM SULFATE, 15% GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.071
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2010 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.071 Å / Relative weight: 1
ReflectionResolution: 1.57→41.04 Å / Num. obs: 23028 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 11 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.13
Reflection shellResolution: 1.57→1.61 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2.02 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE OF SE-MET DERIVATIVE

Resolution: 1.57→41.05 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.64 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. RESIDUES 47-50 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.20414 1152 5 %RANDOM
Rwork0.17581 ---
obs0.17724 21876 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.893 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å2-0.82 Å20 Å2
2---1.65 Å20 Å2
3---2.47 Å2
Refinement stepCycle: LAST / Resolution: 1.57→41.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 0 12 55 1091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0221173
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5271.961600
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0815157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53224.84866
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49915218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.89158
X-RAY DIFFRACTIONr_chiral_restr0.2380.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021926
X-RAY DIFFRACTIONr_gen_planes_other
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_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8351.5688
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.30121132
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.6373485
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.1554.5454
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.8431173
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 82 -
Rwork0.29 1564 -
obs--100 %
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)
10.35-0.17290.27744.1228-0.56720.59030.0765-0.034-0.04090.13470.00410.27560.0296-0.0619-0.08060.1109-0.00640.01890.05190.0160.035731.9711.447.361
20.32850.38240.73833.44552.55293.03480.07060.02380.05-0.4685-0.0619-0.4278-0.00710.0262-0.00870.25070.0270.11510.05760.02780.136239.887-9.862-3.913
30.4259-0.30810.19632.20080.15551.02210.03950.0177-0.03460.1457-0.0203-0.0185-0.0239-0.057-0.01920.0843-0.004-0.03040.0370.00860.0336.276-8.4078.509
46.85038.1667-4.910516.19962.205311.5916-0.39720.7820.4577-0.74280.12921.1910.0772-1.18820.2680.12870.0278-0.18090.243-0.09810.317323.989-14.955-0.996
5102.601242.557469.985819.87453.446888.8993.7742-7.07841.86933.5975-2.66483.0487-3.2466-4.7976-1.10941.022-0.28290.60651.059-0.26730.903822.084-12.65113.728
61.04920.93862.4333.91522.46596.5847-0.00380.0287-0.0298-0.12110.01750.2896-0.11220.0399-0.01380.09880.0083-0.03730.0499-0.00530.042530.77-9.1683.818
75.4729-2.28011.63161.6418-1.269615.31290.20010.1508-0.267-0.1908-0.08610.17050.5526-0.346-0.11410.19760.0349-0.08120.0606-0.03130.078330.436-18.719-1.31
80.82620.6533-0.11723.55881.3760.81760.08-0.0844-0.11950.2118-0.0716-0.15060.0612-0.0122-0.00840.1079-0.0051-0.06180.04130.02110.047541.192-14.70312.803
92.75410.9061-0.40581.7886-0.89673.30880.04150.0955-0.2556-0.05570.0353-0.18180.19820.0432-0.07680.060.017-0.02910.0139-0.01260.082643.744-21.3443.823
101.0463.39031.229312.06394.26951.51110.02410.0327-0.1324-0.2260.091-0.3919-0.05320.0352-0.11510.149-0.00280.02420.03480.00920.076941.018-16.067-1.42
112.53733.3941-0.39734.9184-0.85210.2875-0.00780.1291-0.5987-0.007-0.0957-0.8517-0.0060.14360.10350.0702-0.01450.06150.26250.03780.238852.71510.171.666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 11
2X-RAY DIFFRACTION2A12 - 25
3X-RAY DIFFRACTION3A26 - 36
4X-RAY DIFFRACTION4A37 - 42
5X-RAY DIFFRACTION5A43 - 51
6X-RAY DIFFRACTION6A52 - 60
7X-RAY DIFFRACTION7A61 - 67
8X-RAY DIFFRACTION8A68 - 81
9X-RAY DIFFRACTION9A82 - 97
10X-RAY DIFFRACTION10A98 - 106
11X-RAY DIFFRACTION11A107 - 126

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