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- PDB-2vix: Methylated Shigella flexneri MxiC -

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Basic information

Entry
Database: PDB / ID: 2vix
TitleMethylated Shigella flexneri MxiC
ComponentsPROTEIN MXIC
KeywordsTRANSPORT PROTEIN / SECRETION REGULATION / T3SS / VIRULENCE / TYPE THREE SECRETION SYSTEM
Function / homology
Function and homology information


protein secretion by the type III secretion system / outer membrane / negative regulation of protein secretion / host cell / cell surface / extracellular region
Similarity search - Function
Arc Repressor Mutant, subunit A - #2060 / DNA polymerase; domain 1 - #630 / Monooxygenase - #240 / Salmonella/Shigella invasion protein E / : / Protein MxiC, C-terminal / Type III secretion regulator, YopN/LcrE/InvE/MxiC / Hypersensitivity response secretion-like, HrpJ / HrpJ-like domain / Monooxygenase ...Arc Repressor Mutant, subunit A - #2060 / DNA polymerase; domain 1 - #630 / Monooxygenase - #240 / Salmonella/Shigella invasion protein E / : / Protein MxiC, C-terminal / Type III secretion regulator, YopN/LcrE/InvE/MxiC / Hypersensitivity response secretion-like, HrpJ / HrpJ-like domain / Monooxygenase / DNA polymerase; domain 1 / Arc Repressor Mutant, subunit A / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Protein MxiC
Similarity search - Component
Biological speciesSHIGELLA FLEXNERI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsDeane, J.E. / Roversi, P. / King, C. / Johnson, S. / Lea, S.M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structures of the Shigella Flexneri Type 3 Secretion System Protein Mxic Reveal Conformational Variability Amongst Homologues.
Authors: Deane, J.E. / Roversi, P. / King, C. / Johnson, S. / Lea, S.M.
History
DepositionDec 5, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: PROTEIN MXIC
B: PROTEIN MXIC
C: PROTEIN MXIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7966
Polymers102,5533
Non-polymers2433
Water2,414134
1
A: PROTEIN MXIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3353
Polymers34,1841
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN MXIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2762
Polymers34,1841
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PROTEIN MXIC


Theoretical massNumber of molelcules
Total (without water)34,1841
Polymers34,1841
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.791, 102.572, 122.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.86493, 0.49667, -0.07229), (-0.26183, -0.5694, -0.77925), (-0.42819, -0.65507, 0.62253)-38.81416, 51.93637, 58.57495
2given(-0.99818, 0.03285, 0.05053), (0.06026, 0.53099, 0.84523), (0.00094, 0.84674, -0.53201)-15.65585, 13.38861, -22.48606

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Components

#1: Protein PROTEIN MXIC / MXIC


Mass: 34184.215 Da / Num. of mol.: 3 / Fragment: RESIDUES 74-355
Source method: isolated from a genetically manipulated source
Details: THE CONSTRUCT IS A DELETION OF THE FIRST 73 RESIDUES AND WAS METHYLATED CHEMICALLY FOLLOWING WALTER ET AL, STRUCTURE 14,1617-1622 (2006)
Source: (gene. exp.) SHIGELLA FLEXNERI (bacteria) / Strain: PWR100 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q04640
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsN-DIMETHYL-LYSINE (MLY): GENERATED FOLLOWING THE METHYLATION PROTOCOL DESCRIBED IN WALTERS ET AL. ...N-DIMETHYL-LYSINE (MLY): GENERATED FOLLOWING THE METHYLATION PROTOCOL DESCRIBED IN WALTERS ET AL. STRUCTURE 14, 1617-1622, 2006
Sequence detailsTHE CONSTRUCT IS A DELETION OF RESIDUES 1-73 AND THEN HAS THE SEQUENCE HSSGLVPRGSHM FROM THE ...THE CONSTRUCT IS A DELETION OF RESIDUES 1-73 AND THEN HAS THE SEQUENCE HSSGLVPRGSHM FROM THE EXPRESSION VECTOR.

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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: 2.95 Å3/Da / Density % sol: 58.4 %
Description: THE SEARCH MODEL WAS A LOW-RESOLUTION MODEL TRACED IN THE DENSITY FROM A SEMET CRYSTAL
Crystal growpH: 7.5
Details: 0.2M NAACETATE, 0.1 BISTRIS PROPANE PH 7.5, 20% PEG3350

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9757
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9757 Å / Relative weight: 1
ReflectionResolution: 2.85→50.4 Å / Num. obs: 84697 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 65.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.7
Reflection shellResolution: 2.85→3 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.4 / % possible all: 93.3

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Processing

Software
NameVersionClassification
TNT5.13.1.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→50.4 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: REFINED IN BUSTER-TNT VERSION 2.1.1 WITH RESTRAINTS FROM A MODEL REFINED IN REFMAC5
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1314 0.1 %0.245
Rwork0.244 ---
all0.245 ---
obs0.244 25054 --
Solvent computationSolvent model: BABINET SCALING / Bsol: 60 Å2 / ksol: 0.211 e/Å3
Refinement stepCycle: LAST / Resolution: 2.85→50.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6959 0 16 134 7109
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.006141555
X-RAY DIFFRACTIONt_angle_deg0.821190575
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0034195
X-RAY DIFFRACTIONt_gen_planes0.02119465
X-RAY DIFFRACTIONt_it1.91355520
X-RAY DIFFRACTIONt_nbd0.0493515
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
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_contact

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