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- PDB-3rmr: Crystal structure of Hyaloperonospora arabidopsidis ATR1 effector... -

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Basic information

Entry
Database: PDB / ID: 3rmr
TitleCrystal structure of Hyaloperonospora arabidopsidis ATR1 effector domain
ComponentsAvirulence protein
KeywordsPROTEIN BINDING / effector / RPP1-recognized / alpha-helical / W-motif / seahorse / virulence / RPP1 / R-protein
Function / homology
Function and homology information


effector-mediated perturbation of host process by symbiont / host cell cytoplasm / host cell nucleus / extracellular region
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2710 / : / : / Avirulence protein ATR1, WY-domain / ATR1 N-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Avirulence protein ATR1 / Avirulence protein ATR1
Similarity search - Component
Biological speciesHyaloperonospora parasitica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsChou, S. / Krasileva, K.V. / Holton, J.M. / Staskawicz, B.J. / Alber, T.
CitationJournal: To be Published
Title: The Hyaloperonospora arabidopsidis ATR1 effector has distributed recognition surfaces and a structural subdomain conserved across oomycete species
Authors: Chou, S. / Krasileva, K.V. / Holton, J.M. / Steinbrenner, A. / Alber, T. / Staskawicz, B.J.
History
DepositionApr 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_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
C: Avirulence protein


Theoretical massNumber of molelcules
Total (without water)89,0303
Polymers89,0303
Non-polymers00
Water6,575365
1
A: Avirulence protein


Theoretical massNumber of molelcules
Total (without water)29,6771
Polymers29,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Avirulence protein


Theoretical massNumber of molelcules
Total (without water)29,6771
Polymers29,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Avirulence protein


Theoretical massNumber of molelcules
Total (without water)29,6771
Polymers29,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Avirulence protein
B: Avirulence protein
C: Avirulence protein

A: Avirulence protein
B: Avirulence protein
C: Avirulence protein


Theoretical massNumber of molelcules
Total (without water)178,0606
Polymers178,0606
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area24230 Å2
ΔGint-179 kcal/mol
Surface area61650 Å2
MethodPISA
5
B: Avirulence protein

A: Avirulence protein
C: Avirulence protein


Theoretical massNumber of molelcules
Total (without water)89,0303
Polymers89,0303
Non-polymers00
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation12_565x,x-y+1,-z+1/61
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-70 kcal/mol
Surface area35730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.432, 119.432, 312.572
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-337-

HOH

21A-346-

HOH

31A-367-

HOH

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Components

#1: Protein Avirulence protein / ATR1


Mass: 29676.621 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hyaloperonospora parasitica (eukaryote)
Gene: Atr1, ATR1NdWsB / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q4VKJ6, UniProt: M4B6G6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Crystal growth in 1.6 M magnesium sulfate, 0.1 M MES, pH 6.5. 1:20000 seeding in 1.2 M magnesium sulfate, 0.01% acetonitrile, 0.1 M MES, pH 5.0. Dehydration in 1.5 M magnesium sulfate, 0.1 M ...Details: Crystal growth in 1.6 M magnesium sulfate, 0.1 M MES, pH 6.5. 1:20000 seeding in 1.2 M magnesium sulfate, 0.01% acetonitrile, 0.1 M MES, pH 5.0. Dehydration in 1.5 M magnesium sulfate, 0.1 M MES, pH 5.0 for 2 hours, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.0722, 1.0631, 1.11587
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2010
RadiationMonochromator: KHOZU double flat crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.07221
21.06311
31.115871
ReflectionResolution: 2.268→103.431 Å / Num. all: 60675 / Num. obs: 57939 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 15.5 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 35.55
Reflection shellResolution: 2.42→2.51 Å / Redundancy: 15.6 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 4.375 / Rsym value: 0.729 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data collection
PHENIXAutoSolmodel building
ELVESrefinement
ELVESdata reduction
HKL-2000data reduction
ELVESdata scaling
HKL-2000data scaling
PHENIXAutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→62.349 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 26.31 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2598 2796 5.03 %
Rwork0.2231 --
obs0.225 55573 93.54 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.454 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.1263 Å2-0 Å20 Å2
2---2.1263 Å2-0 Å2
3---4.2527 Å2
Refinement stepCycle: LAST / Resolution: 2.3→62.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5463 0 0 365 5828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156007
X-RAY DIFFRACTIONf_angle_d1.0227688
X-RAY DIFFRACTIONf_dihedral_angle_d16.2322024
X-RAY DIFFRACTIONf_chiral_restr0.072852
X-RAY DIFFRACTIONf_plane_restr0.004992
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.33970.3343990.31231806X-RAY DIFFRACTION66
2.3397-2.38230.35171020.32252019X-RAY DIFFRACTION74
2.3823-2.42810.33381350.31172328X-RAY DIFFRACTION84
2.4281-2.47760.41711090.30312515X-RAY DIFFRACTION90
2.4776-2.53150.37791380.29142535X-RAY DIFFRACTION91
2.5315-2.59040.33151500.27632576X-RAY DIFFRACTION93
2.5904-2.65520.32681600.26662602X-RAY DIFFRACTION94
2.6552-2.7270.35071500.25662632X-RAY DIFFRACTION95
2.727-2.80720.31741390.24612660X-RAY DIFFRACTION96
2.8072-2.89780.27131310.24192720X-RAY DIFFRACTION97
2.8978-3.00140.28751300.23552726X-RAY DIFFRACTION97
3.0014-3.12160.28091280.24172741X-RAY DIFFRACTION97
3.1216-3.26360.31071450.23642771X-RAY DIFFRACTION99
3.2636-3.43570.26881510.22722776X-RAY DIFFRACTION99
3.4357-3.65090.24871370.21722799X-RAY DIFFRACTION99
3.6509-3.93280.23011560.18912812X-RAY DIFFRACTION99
3.9328-4.32850.22581480.17592856X-RAY DIFFRACTION100
4.3285-4.95460.19931690.18212858X-RAY DIFFRACTION100
4.9546-6.24130.23991520.21362932X-RAY DIFFRACTION99
6.2413-62.37210.221670.22023113X-RAY DIFFRACTION99

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