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- PDB-4b6x: Crystal structure of in planta processed AvrRps4 -

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Basic information

Entry
Database: PDB / ID: 4b6x
TitleCrystal structure of in planta processed AvrRps4
ComponentsAVIRULENCE PROTEIN
KeywordsTOXIN / TYPE 3 SECRETED EFFECTOR
Function / homology: / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / ACETATE ION / Avirulence protein
Function and homology information
Biological speciesPSEUDOMONAS SYRINGAE PV. PISI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsSohn, K.H. / Hughes, R.K. / Piquerez, S.J. / Jones, J.D.G. / Banfield, M.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Distinct Regions of the Pseudomonas Syringae Coiled-Coil Effector Avrrps4 are Required for Activation of Immunity.
Authors: Sohn, K.H. / Hughes, R.K. / Piquerez, S.J. / Jones, J.D.G. / Banfield, M.J.
History
DepositionAug 15, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references / Structure summary
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: AVIRULENCE PROTEIN
B: AVIRULENCE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2533
Polymers20,1942
Non-polymers591
Water1,67593
1
A: AVIRULENCE PROTEIN


Theoretical massNumber of molelcules
Total (without water)10,0971
Polymers10,0971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: AVIRULENCE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1562
Polymers10,0971
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.690, 64.690, 73.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11B-2012-

HOH

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Components

#1: Protein AVIRULENCE PROTEIN / AVRRPS4


Mass: 10097.181 Da / Num. of mol.: 2
Fragment: IN-PLANTA PROCESSED C-TERMINAL DOMAIN, RESIDUES 134-220
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS SYRINGAE PV. PISI (bacteria)
Plasmid: POPIN-F / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q52432
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONSTRUCT CRYSTALLIZED IS THE IN PLANTA PROCESSED C- TERMINAL DOMAIN (RESIDUES 134 - 221). N- ...CONSTRUCT CRYSTALLIZED IS THE IN PLANTA PROCESSED C- TERMINAL DOMAIN (RESIDUES 134 - 221). N-TERMINAL RESIDUES 'GP' ARE DERIVED FROM THE EXPRESSION VECTOR.

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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: 2.19 Å3/Da / Density % sol: 43.93 % / Description: NONE
Crystal growpH: 5.2
Details: 14-16% 2-METHYL-2,4-PENTANDIOL (MPD) BUFFERED WITH 100 MM SODIUM ACETATE PH 5.1-5.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.94
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2.2→56 Å / Num. obs: 9120 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.2→56.02 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.174 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19052 693 7.6 %RANDOM
Rwork0.16118 ---
obs0.16358 8412 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.33 Å20 Å2
2--0.66 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 2.2→56.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1010 0 4 93 1107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211044
X-RAY DIFFRACTIONr_bond_other_d0.0010.02710
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9561412
X-RAY DIFFRACTIONr_angle_other_deg0.89831723
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4485133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.6282568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17315195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8671515
X-RAY DIFFRACTIONr_chiral_restr0.0720.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021210
X-RAY DIFFRACTIONr_gen_planes_other00.02201
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_it0.6861.5649
X-RAY DIFFRACTIONr_mcbond_other0.2051.5256
X-RAY DIFFRACTIONr_mcangle_it1.31621032
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6213395
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1884.5376
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 59 -
Rwork0.183 615 -
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)
13.38511.1526-4.67911.0688-1.61448.7746-0.0419-0.2834-0.1040.0025-0.1025-0.14440.2090.57110.14450.02740.0078-0.03160.08390.01310.077312.016933.041422.9232
29.2655-1.82916.54362.19-1.04369.8086-0.107-0.78870.10120.23850.0874-0.2095-0.0349-0.22560.01960.0419-0.0379-0.0180.1983-0.01860.121323.847941.223423.8863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A153 - 221
2X-RAY DIFFRACTION2B156 - 213

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