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- PDB-4a56: Crystal structure of the type 2 secretion system pilotin from Kle... -

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Basic information

Entry
Database: PDB / ID: 4a56
TitleCrystal structure of the type 2 secretion system pilotin from Klebsiella Oxytoca
ComponentsPULLULANASE SECRETION PROTEIN PULS
KeywordsPROTEIN TRANSPORT / T2SS
Function / homology
Function and homology information


cell outer membrane / intracellular protein transport
Similarity search - Function
Chaperone lipoprotein PulS/OutS / Chaperone lipoprotein, PulS/OutS / Chaperone lipoprotein, PulS/OutS-like / PulS/OutS-like superfamily / Type II secretion system pilotin lipoprotein (PulS_OutS) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Pullulanase secretion protein puls / Pullulanase secretion protein PulS
Similarity search - Component
Biological speciesKLEBSIELLA OXYTOCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.24 Å
AuthorsTosi, T. / Nickerson, N.N. / Mollica, L. / RingkjobingJensen, M. / Blackledge, M. / Baron, B. / England, P. / Pugsley, A.P. / Dessen, A.
CitationJournal: Mol.Microbiol / Year: 2011
Title: Pilotin-Secretin Recognition in the Type II Secretion System of Klebsiella Oxytoca.
Authors: Tosi, T. / Nickerson, N.N. / Mollica, L. / Jensen, M.R. / Blackledge, M. / Baron, B. / England, P. / Pugsley, A.P. / Dessen, A.
History
DepositionOct 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PULLULANASE SECRETION PROTEIN PULS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3622
Polymers10,2431
Non-polymers1181
Water1,49583
1
A: PULLULANASE SECRETION PROTEIN PULS
hetero molecules

A: PULLULANASE SECRETION PROTEIN PULS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7234
Polymers20,4872
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area1780 Å2
ΔGint-21 kcal/mol
Surface area9850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.507, 46.896, 109.686
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2025-

HOH

21A-2033-

HOH

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Components

#1: Protein PULLULANASE SECRETION PROTEIN PULS / PULS


Mass: 10243.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RESIDUES 30-122 / Source: (gene. exp.) KLEBSIELLA OXYTOCA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20440, UniProt: H0USY9*PLUS
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.83 % / Description: NONE
Crystal growpH: 7.5 / Details: 100 MM HEPES PH 7.5, 75% MPD

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Data collection

DiffractionMean temperature: 230 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.24→4 Å / Num. obs: 47490 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 21 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.02 / Rsym value: 0.05 / Net I/σ(I): 52

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.24→54.84 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.201 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18975 1276 5.1 %RANDOM
Rwork0.17322 ---
obs0.17406 23774 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.246 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.24→54.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms717 0 8 83 808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022790
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9631081
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0275111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.2192542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17315146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.591158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021608
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_it0.8861.5493
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6682794
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5583297
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1634.5277
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: 1.242→1.275 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 73 -
Rwork0.218 1400 -
obs--79.45 %
Refinement TLS params.Method: refined / Origin x: -9.0237 Å / Origin y: 12.215 Å / Origin z: 16.2778 Å
111213212223313233
T0.0117 Å20.0115 Å20.0074 Å2-0.0191 Å20.0076 Å2--0.0216 Å2
L0.1638 °2-0.2276 °2-0.0652 °2-0.6684 °20.5193 °2--0.7402 °2
S0.0279 Å °0.0483 Å °0.0411 Å °-0.0111 Å °-0.049 Å °-0.0426 Å °-0.0018 Å °-0.0213 Å °0.0211 Å °

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