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- PDB-3i0u: Structure of the type III effector/phosphothreonine lyase OspF fr... -

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Basic information

Entry
Database: PDB / ID: 3i0u
TitleStructure of the type III effector/phosphothreonine lyase OspF from Shigella flexneri
ComponentsPhosphothreonine lyase ospF
KeywordsLYASE / Shigella flexneri / apo-structure / type III effector / phosphothreonine lyase / Secreted / Virulence / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Acting on phosphates / lyase activity / extracellular region
Similarity search - Function
Phosphothreonine lyase fold / phosphothreonine lyase / OspF/SpvC / OspF/SpvC superfamily / Salmonella virulence-associated 28kDa protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphothreonine lyase OspF
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsSinger, A.U. / Skarina, T. / Nocek, B. / Gordon, R. / Lam, R. / Kagan, O. / Edwards, A.M. / Joachimiak, A. / Chirgadze, N.Y. / Anderson, W.F. ...Singer, A.U. / Skarina, T. / Nocek, B. / Gordon, R. / Lam, R. / Kagan, O. / Edwards, A.M. / Joachimiak, A. / Chirgadze, N.Y. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Structure of the type III effector/phosphothreonine lyase OspF from Shigella flexneri
Authors: Singer, A.U. / Skarina, T. / Lam, R. / Gordon, R. / Nocek, B. / Kagan, O. / Edwards, A.M. / Chirgadze, N.Y. / Parsot, C. / Arbibe, L. / Savchenko, A.
History
DepositionJun 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

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Assembly

Deposited unit
A: Phosphothreonine lyase ospF
B: Phosphothreonine lyase ospF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9603
Polymers50,8412
Non-polymers1181
Water1086
1
A: Phosphothreonine lyase ospF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5392
Polymers25,4211
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphothreonine lyase ospF


Theoretical massNumber of molelcules
Total (without water)25,4211
Polymers25,4211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.125, 62.125, 239.586
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A20 - 240
2111B20 - 240

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Components

#1: Protein Phosphothreonine lyase ospF / Effector protein ospF


Mass: 25420.729 Da / Num. of mol.: 2 / Fragment: OspF residues 23-239
Source method: isolated from a genetically manipulated source
Details: TEV cleavage / Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: 2a / Gene: CP0010, mkaD, ospF, pWR501_0013, SFLP011 / Plasmid: p15Tvlic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL
References: UniProt: Q8VSP9, Lyases; Carbon-oxygen lyases; Acting on phosphates
#2: Chemical ChemComp-MPD / (4S)-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


Mass: 18.015 Da / Num. of mol.: 6 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2745.9
2
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% isopropanol, 20% PEG4K, 1% PEG6K, 0.5% 2-methyl-2,4-pentanediol, 0.1 M HEPES pH 7.5. Cryoprotected in Paratone-N oil, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97929
SYNCHROTRONAPS 19-ID20.97924, 0.97940
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDNov 26, 2007mirrors
ADSC QUANTUM 3152CCDFeb 27, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI-111 CHANNELSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.979241
30.97941
ReflectionResolution: 2.7→50 Å / Num. all: 13796 / Num. obs: 13771 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 48.01
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 7.14 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHELXSphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→43.94 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.915 / SU B: 38.746 / SU ML: 0.361 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 2.782 / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The MAD dataset was used to solve the structure, but the structure was REFINED on a single wavelength dataset refined to 2.7A
RfactorNum. reflection% reflectionSelection details
Rfree0.28726 673 4.9 %RANDOM
Rwork0.24968 ---
obs0.25158 13027 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.7→43.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3193 0 8 6 3207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223274
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.9524426
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8185386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72924170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.71115551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.591522
X-RAY DIFFRACTIONr_chiral_restr0.1130.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022529
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1710.31304
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.52255
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.5167
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.359
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4140.55
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4311.52005
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.65223164
X-RAY DIFFRACTIONr_scbond_it1.24231438
X-RAY DIFFRACTIONr_scangle_it1.7324.51262
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1530 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.080.05
tight thermal0.160.5
LS refinement shellResolution: 2.701→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 43 -
Rwork0.264 920 -
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)
16.33220.3704-2.63175.21031.62266.895-0.3270.5802-0.7317-0.07230.138-0.26010.0348-0.16550.1891-0.43540.1194-0.0684-0.1081-0.1814-0.15980.53916.4774101.6295
21.8877-0.12570.35888.6493.89366.29560.09810.648-0.00790.09190.2393-0.54880.11630.653-0.3375-0.31070.2333-0.00130.06630.0128-0.234827.614446.9178107.2051
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 239
2X-RAY DIFFRACTION2B27 - 239

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