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- PDB-5fqu: Orthorhombic crystal structure of of PlpD (selenomethionine deriv... -

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Basic information

Entry
Database: PDB / ID: 5fqu
TitleOrthorhombic crystal structure of of PlpD (selenomethionine derivative)
ComponentsPATATIN-LIKE PROTEIN, PLPD
KeywordsTRANSPORT PROTEIN / BACTERIAL SECRETION / PHOSPHOLIPASE / LIPID AFFINITY / INFECTION
Function / homology
Function and homology information


protein secretion by the type V secretion system / lipase activity / lipid catabolic process / cell outer membrane / extracellular region
Similarity search - Function
Patatin-like phospholipase domain / Patatin-like phospholipase / Patatin-like phospholipase (PNPLA) domain profile. / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Bacterial surface antigen (D15) / Omp85 superfamily domain / Acyl transferase/acyl hydrolase/lysophospholipase
Similarity search - Domain/homology
AZIDE ION / Patatin-like protein, PlpD
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.74 Å
AuthorsVinicius da Mata Madeira, P. / Zouhir, S. / Basso, P. / Neves, D. / Laubier, A. / Salacha, R. / Bleves, S. / Faudry, E. / Contreras-Martel, C. / Dessen, A.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structural Basis of Lipid Targeting and Destruction by the Type V Secretion System of Pseudomonas Aeruginosa.
Authors: Da Mata Madeira, P.V. / Zouhir, S. / Basso, P. / Neves, D. / Laubier, A. / Salacha, R. / Bleves, S. / Faudry, E. / Contreras-Martel, C. / Dessen, A.
History
DepositionDec 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PATATIN-LIKE PROTEIN, PLPD
B: PATATIN-LIKE PROTEIN, PLPD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6645
Polymers68,5762
Non-polymers883
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-44.4 kcal/mol
Surface area21110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.743, 113.393, 130.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PATATIN-LIKE PROTEIN, PLPD


Mass: 34288.105 Da / Num. of mol.: 2 / Fragment: PASSENGER DOMAIN, UNP RESIDUES 20-333
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q9HYQ6
#2: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSELENOMETHIONINE DERIVATIVE

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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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growDetails: 20%W/V PEG3350, 200MM SODIUM NITRATE, 0.6% N-DODECYL-BETA-D MALTOSIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97939
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 2.74→85.58 Å / Num. obs: 19015 / % possible obs: 99.5 % / Observed criterion σ(I): 2.8 / Redundancy: 4.5 % / Biso Wilson estimate: 46.511 Å2 / Rsym value: 0.01 / Net I/σ(I): 10.42
Reflection shellResolution: 2.74→2.9 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.81 / Rsym value: 0.54 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.74→85.57 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 19.334 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R: 0.629 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23801 968 5.1 %RANDOM
Rwork0.19579 ---
obs0.19805 17914 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.713 Å2
Baniso -1Baniso -2Baniso -3
1--9.82 Å20 Å20 Å2
2--18.06 Å20 Å2
3----8.24 Å2
Refinement stepCycle: LAST / Resolution: 2.74→85.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3702 0 5 61 3768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193750
X-RAY DIFFRACTIONr_bond_other_d0.0030.023785
X-RAY DIFFRACTIONr_angle_refined_deg1.4162.0035086
X-RAY DIFFRACTIONr_angle_other_deg0.86638669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9415491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.12124.028144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.9115594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3081530
X-RAY DIFFRACTIONr_chiral_restr0.0770.2620
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214217
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02769
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_it6.5966.5581982
X-RAY DIFFRACTIONr_mcbond_other6.5766.5571981
X-RAY DIFFRACTIONr_mcangle_it9.4519.8232467
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.1947.3531768
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.736→2.807 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 62 -
Rwork0.444 1209 -
obs--93.52 %

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