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- PDB-3svi: Structure of the Pto-binding domain of HopPmaL generated by limit... -

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Basic information

Entry
Database: PDB / ID: 3svi
TitleStructure of the Pto-binding domain of HopPmaL generated by limited thermolysin digestion
ComponentsType III effector HopAB2
KeywordsSIGNALING PROTEIN / type III effector / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / helical bundle
Function / homologyMonooxygenase - #110 / Effector protein HopAB, Pto-binding domain / Monooxygenase / Up-down Bundle / Mainly Alpha / Type III effector HopAB2
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsSinger, A.U. / Stein, A. / Xu, X. / Cui, H. / Joachimiak, A. / Edwards, A.M. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Biochemistry / Year: 2012
Title: Structural Analysis of HopPmaL Reveals the Presence of a Second Adaptor Domain Common to the HopAB Family of Pseudomonas syringae Type III Effectors.
Authors: Singer, A.U. / Wu, B. / Yee, A. / Houliston, S. / Xu, X. / Cui, H. / Skarina, T. / Garcia, M. / Semesi, A. / Arrowsmith, C.H. / Savchenko, A.
History
DepositionJul 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Jan 25, 2012Group: Database references
Revision 1.3Feb 29, 2012Group: Structure summary
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Type III effector HopAB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9388
Polymers9,5811
Non-polymers3577
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Type III effector HopAB2
hetero molecules

A: Type III effector HopAB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,87716
Polymers19,1632
Non-polymers71414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2740 Å2
ΔGint-135 kcal/mol
Surface area9100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.277, 57.277, 55.658
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-82-

HOH

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Components

#1: Protein Type III effector HopAB2


Mass: 9581.355 Da / Num. of mol.: 1 / Fragment: sequence database residues 72-156
Source method: isolated from a genetically manipulated source
Details: protein was cut with TEV, then treated with limiting amounts of thermolysin during crystallization
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Strain: pv. maculicola strain ES4326 / Gene: HopPmaL, PMA4326_19338 / Plasmid: p15TvLic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIPL / References: UniProt: F3HNN9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Hepes ph7.5, 0.1M NaCl, 1.6M Ammonium Sulphate, 0.2 mg/ml thermolysin was added to the protein mixture. Paratone-N oil was used for cryoprotection, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2009 / Details: mirrors
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.75→25.615 Å / Num. obs: 9824 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 43.429
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.9 / Num. unique all: 477 / Rsym value: 0.428 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXCDphasing
SHELXEmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→25.615 Å / SU ML: 0.36 / Isotropic thermal model: Isotropic / σ(F): 1.35 / σ(I): 0 / Phase error: 19.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 432 4.78 %RANDOM
Rwork0.1859 ---
obs0.1874 9038 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.16 Å2 / ksol: 0.379 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms624 0 15 71 710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007694
X-RAY DIFFRACTIONf_angle_d1.009940
X-RAY DIFFRACTIONf_dihedral_angle_d14.561275
X-RAY DIFFRACTIONf_chiral_restr0.072101
X-RAY DIFFRACTIONf_plane_restr0.006129
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.8001-2.06040.26631420.208527962938
2.0604-2.59550.20271380.165728372975
2.5955-25.61760.21351520.189429733125
Refinement TLS params.Method: refined / Origin x: -14.7794 Å / Origin y: -3.9139 Å / Origin z: 13.8576 Å
111213212223313233
T0.1054 Å2-0.0001 Å2-0.0062 Å2-0.084 Å20.0076 Å2--0.1094 Å2
L1.664 °20.6581 °2-0.0003 °2-1.5276 °20.8613 °2--2.2139 °2
S-0.009 Å °-0.0542 Å °-0.1815 Å °0.1024 Å °-0.0475 Å °-0.1259 Å °0.1863 Å °-0.0669 Å °0.049 Å °
Refinement TLS groupSelection details: (chain A and resid 139:217)

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