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- PDB-1y9l: The X-ray structure of an secretion system protein -

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Basic information

Entry
Database: PDB / ID: 1y9l
TitleThe X-ray structure of an secretion system protein
ComponentsLipoprotein mxiM
KeywordsLIPID BINDING PROTEIN / CRACKED BETA BARREL / MIXED ALPHA/BETA
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Pilot protein MxiM / Pilot protein MxiM / MxiM superfamily / Pilot protein MxiM / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / UNDECANE / Type 3 secretion system pilotin
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsLario, P.I. / Pfuetzer, R.A. / Frey, E.A. / Creagh, L. / Haynes, C. / Maurelli, A.T. / Strynadka, N.C.
CitationJournal: Embo J. / Year: 2005
Title: Structure and biochemical analysis of a secretin pilot protein.
Authors: Lario, P.I. / Pfuetzner, R.A. / Frey, E.A. / Creagh, L. / Haynes, C. / Maurelli, A.T. / Strynadka, N.C.
History
DepositionDec 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Lipoprotein mxiM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1193
Polymers12,9041
Non-polymers2152
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.844, 49.683, 29.487
Angle α, β, γ (deg.)90.00, 102.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Lipoprotein mxiM


Mass: 12903.888 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: mxiM / Plasmid: PET19B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A1X2
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-UND / UNDECANE / LIPID FRAGMENT


Mass: 156.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.06 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: (NH4)2SO4, LiSO4, NaCH3CO2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.0, 0.8981, 0.9794, 0.9796
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2003
Details: a parabolic collimating mirror placed upstream of the monochromator
RadiationMonochromator: CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.89811
30.97941
40.97961
ReflectionResolution: 1.5→20.261 Å / Num. all: 18869 / Num. obs: 18209 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 22.6 Å2 / Rsym value: 0.036 / Net I/σ(I): 16.5
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3 / Rsym value: 0.421 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→20.261 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.181 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25071 929 5.1 %RANDOM
Rwork0.22028 ---
all0.22192 17871 --
obs0.22028 17235 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.229 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.14 Å2
2--0.61 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 15 98 983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022956
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9751296
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7065129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83626.2540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71915188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.344151
X-RAY DIFFRACTIONr_chiral_restr0.1060.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02700
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.2436
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.2656
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.270
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0791.5601
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5562943
X-RAY DIFFRACTIONr_scbond_it2.423408
X-RAY DIFFRACTIONr_scangle_it3.4524.5343
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 67 -
Rwork0.238 1314 -
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)
12.2628-0.28550.41731.38730.6750.5702-0.0366-0.0842-0.03720.10930.08040.07620.04820.0565-0.0438-0.01310.01720.0142-0.02370.0077-0.05326.536142.19352.9441
2299.8457209.2428-219.7288194.8876-102.2383214.4418-0.4287-1.2033-0.39390.97760.25340.66971.58642.1720.17520.0206-0.0176-0.01250.00940.02120.004822.124142.02176.9394
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA33 - 1426 - 115
2X-RAY DIFFRACTION2AC150

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