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- PDB-4qmk: Crystal structure of type III effector protein ExoU (exoU) -

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Basic information

Entry
Database: PDB / ID: 4qmk
TitleCrystal structure of type III effector protein ExoU (exoU)
ComponentsType III secretion system effector protein ExoU
KeywordsTOXIN / type III secretion system / Pseudomonas fluorescens A506 / type III effector protein ExoU / Infectious Diseases / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases / membrane localization domain / PLA2 domain / patatin-like phospholipase domain
Function / homology
Function and homology information


Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #100 / Cytosolic phospholipase A2 catalytic domain / Cytosolic phospholipase A2 catalytic domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / :
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHalavaty, A.S. / Tyson, G.H. / Zhang, A. / Hauser, A.R. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Biol.Chem. / Year: 2015
Title: A Novel Phosphatidylinositol 4,5-Bisphosphate Binding Domain Mediates Plasma Membrane Localization of ExoU and Other Patatin-like Phospholipases.
Authors: Tyson, G.H. / Halavaty, A.S. / Kim, H. / Geissler, B. / Agard, M. / Satchell, K.J. / Cho, W. / Anderson, W.F. / Hauser, A.R.
History
DepositionJun 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 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_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: Type III secretion system effector protein ExoU
B: Type III secretion system effector protein ExoU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,6143
Polymers145,5362
Non-polymers781
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-20 kcal/mol
Surface area49620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.218, 115.341, 88.443
Angle α, β, γ (deg.)90.00, 102.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 22 - 639 / Label seq-ID: 34 - 651

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Type III secretion system effector protein ExoU


Mass: 72768.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: A506 / Gene: exoU, PflA506_5017 / Plasmid: pEcoli (from Clontech) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/Magic / References: UniProt: I2BZ03
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.3 Å3/Da / Density % sol: 46.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: protein: 5.8 mg/ml in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 5 mM BME. Crystallization conditions: The Classics II Suite (#G7:79): 0.2 M Ammonium acetate, 0.1 M Bis-Tris (pH 6.5), 25% (w/v) PEG ...Details: protein: 5.8 mg/ml in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 5 mM BME. Crystallization conditions: The Classics II Suite (#G7:79): 0.2 M Ammonium acetate, 0.1 M Bis-Tris (pH 6.5), 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2013 / Details: Be Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 43226 / Num. obs: 43226 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 54.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.7
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2.05 / Num. unique all: 1696 / % possible all: 75.7

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TU3

3tu3


Resolution: 2.5→29.86 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / SU B: 21.65 / SU ML: 0.231 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.527 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26978 2190 5.1 %RANDOM
Rwork0.2059 ---
obs0.20912 41015 94.83 %-
all-41015 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.685 Å2
Baniso -1Baniso -2Baniso -3
1-3.35 Å20 Å2-5.52 Å2
2--2.7 Å20 Å2
3----4.35 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7904 0 4 206 8114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198079
X-RAY DIFFRACTIONr_bond_other_d0.0040.028017
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.98310941
X-RAY DIFFRACTIONr_angle_other_deg0.979318402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.92851031
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45624.27356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.085151406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6411571
X-RAY DIFFRACTIONr_chiral_restr0.0950.21261
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219197
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021758
Refine LS restraints NCS

Ens-ID: 1 / Number: 29380 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 136 -
Rwork0.324 2344 -
obs-2344 74.05 %
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)
11.04310.40760.12221.1019-1.50783.5106-0.02640.1015-0.0082-0.1822-0.0004-0.14650.44190.29950.02680.1350.05280.09750.066-0.03090.221421.569615.570138.3331
23.059-0.0622-0.77320.02570.12882.1086-0.0110.32830.1841-0.0396-0.0151-0.00510.08410.00180.02610.1762-0.02320.09480.20670.080.25097.881432.930915.7826
32.5105-1.5657-0.41973.70530.71462.28230.11060.2519-0.1594-0.2608-0.01010.18320.38190.0737-0.10050.1713-0.00890.05910.095-0.05010.178813.378617.563118.9048
41.52951.1062-0.3012.22-1.29431.31630.00020.09280.03440.0511-0.0521-0.14850.03390.17590.0520.08190.00050.08740.0562-0.02220.196720.140817.464242.9745
53.3284-0.28981.61424.0934-0.37794.41510.06950.2194-0.0399-0.21240.01940.30960.1056-0.0425-0.08890.1031-0.00090.12620.02080.00060.2524-6.0551-3.223935.8539
60.8502-0.98230.24496.4661-0.74822.0613-0.0536-0.03-0.0803-0.07250.10730.32810.0278-0.1196-0.05370.05090.00010.10430.00770.01080.2719-9.176732.333535.2433
71.8905-0.14210.03231.27012.15613.75120.2969-0.2125-0.09470.3408-0.2905-0.04140.7004-0.5159-0.00640.2718-0.08340.07450.12110.03830.1251-22.635712.7838-14.6852
810.38031.7034-0.15870.9293-0.97552.2479-0.07510.3180.00460.1469-0.03470.0203-0.3501-0.42960.10980.0960.04920.06220.3718-0.10.1716-15.196433.363510.4608
91.40651.34811.24474.03270.65784.57570.5519-0.31040.02950.1777-0.2902-0.16561.0798-0.1543-0.26170.3568-0.05860.00940.24650.01040.1353-14.944617.45386.6883
101.6306-0.7178-0.55751.49071.50613.53190.1511-0.23210.23390.1144-0.1349-0.02010.1427-0.4129-0.01620.1007-0.01560.10150.1916-0.03610.1433-25.076820.012-16.7845
112.50690.90130.65622.36141.02831.52750.27180.0968-0.15890.43010.0686-0.23530.42330.4286-0.34040.22990.16760.00840.2422-0.08930.28295.93365.0708-18.0966
124.03890.3574-0.02257.44152.61616.7473-0.10750.05430.0553-0.46980.0965-0.2491-0.83660.41310.0110.1699-0.03480.11570.12690.06720.23391.183538.8155-8.9981
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 116
2X-RAY DIFFRACTION2A117 - 177
3X-RAY DIFFRACTION3A178 - 309
4X-RAY DIFFRACTION4A310 - 459
5X-RAY DIFFRACTION5A460 - 552
6X-RAY DIFFRACTION6A553 - 639
7X-RAY DIFFRACTION7B22 - 116
8X-RAY DIFFRACTION8B117 - 151
9X-RAY DIFFRACTION9B152 - 272
10X-RAY DIFFRACTION10B309 - 429
11X-RAY DIFFRACTION11B430 - 559
12X-RAY DIFFRACTION12B560 - 639

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