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- PDB-1y9t: Crystal structure of a type III secretion system protein complexe... -

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Basic information

Entry
Database: PDB / ID: 1y9t
TitleCrystal structure of a type III secretion system protein complexed with the lipid, 1-monohexanoyl-2-hydroxy-sn-glycero-3-phosphate
ComponentsLipoprotein mxiM
KeywordsLIPID BINDING PROTEIN / MIXED ALPHA/BETA / CRACKED B-BARREL FOLD
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 / (2R)-2-HYDROXY-3-(PHOSPHONOOXY)PROPYL HEXANOATE / Type 3 secretion system pilotin
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.87 Å
AuthorsLario, P.I. / 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 16, 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 1.3Aug 23, 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_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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoprotein mxiM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2333
Polymers12,9041
Non-polymers3292
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.036, 49.721, 29.520
Angle α, β, γ (deg.)90.00, 101.99, 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-HHG / (2R)-2-HYDROXY-3-(PHOSPHONOOXY)PROPYL HEXANOATE / 1-MONOHEXANOYL-2-HYDROXY-SN-GLYCERO-3-PHOSPHATE


Mass: 270.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.3 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: (NH3)2SO4 LiSO4 NaCHOCH3, 1-monohexanoyl-2-hydroxy-sn-glycero-3-phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 10, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.87→42.4 Å / Num. all: 9460 / Num. obs: 9460 / % possible obs: 96.37 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 32.5 Å2 / Rsym value: 0.027 / Net I/σ(I): 34
Reflection shellResolution: 1.87→1.94 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 912 / Rsym value: 0.22 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1Y9L

1y9l


Resolution: 1.87→42.4 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.486 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24907 496 5.2 %EQUIVALENT RFREE REFLECTIONS TO PDB ENTRY 1Y9L (RANDOM)
Rwork0.20613 ---
all0.20843 9301 --
obs0.20843 8964 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.07 Å2
2--0.7 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.87→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms870 0 21 53 944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022955
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9821297
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9185127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47726.2540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50115184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.05151
X-RAY DIFFRACTIONr_chiral_restr0.1050.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02700
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.2411
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2647
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9761.5589
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5312936
X-RAY DIFFRACTIONr_scbond_it2.2683413
X-RAY DIFFRACTIONr_scangle_it3.6034.5352
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.87→1.919 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 25 -
Rwork0.251 637 -
obs-637 93.37 %
Refinement TLS params.Method: refined / Origin x: 26.6107 Å / Origin y: 42.2189 Å / Origin z: 2.9285 Å
111213212223313233
T-0.0341 Å20.0158 Å20.0106 Å2--0.0298 Å20.0024 Å2---0.042 Å2
L1.9162 °2-0.4262 °20.0991 °2-0.9273 °20.5307 °2--0.3722 °2
S-0.0471 Å °-0.0557 Å °-0.0039 Å °0.056 Å °0.0758 Å °0.0546 Å °0.0408 Å °0.0179 Å °-0.0287 Å °

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