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- PDB-6ije: Crystal structure of the type VI amidase immunity (Tai4) from Agr... -

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Basic information

Entry
Database: PDB / ID: 6ije
TitleCrystal structure of the type VI amidase immunity (Tai4) from Agrobacterium tumefaciens
ComponentsTai4
KeywordsANTITOXIN
Function / homologyRap1a immunity protein / Rap1a immunity proteins / Rap1a domain-containing protein
Function and homology information
Biological speciesRhizobium radiobacter (Agrobacterium genomosp. 4)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsFukuhara, S. / Nakane, T. / Yamashita, K. / Ishii, R. / Ishitani, R. / Nureki, O.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structure of the Agrobacterium tumefaciens type VI effector-immunity complex.
Authors: Fukuhara, S. / Nakane, T. / Yamashita, K. / Ishii, R. / Ishitani, R. / Nureki, O.
History
DepositionOct 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Tai4
A: Tai4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8239
Polymers23,3882
Non-polymers4347
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-8 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.921, 57.756, 71.465
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _ / Auth seq-ID: 2 - 99 / Label seq-ID: 7 - 104

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

#1: Protein Tai4


Mass: 11694.150 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium radiobacter (Agrobacterium genomosp. 4)
Gene: SY94_4314 / Plasmid: pCold-GST / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: A0A083ZID3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 48.3 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 33 % PEG 6000, 1.5 M lithium chloride, 100 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→53.92 Å / Num. obs: 32919 / % possible obs: 99.5 % / Redundancy: 6.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.029 / Rrim(I) all: 0.073 / Net I/σ(I): 13 / Num. measured all: 203509 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.55-1.584.20.56815090.8070.3130.65494.7
8.49-53.925.90.0472550.9980.0210.05299.7

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZFI

3zfi


Resolution: 1.55→44.96 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.375 / SU ML: 0.049 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.073
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 1556 4.7 %RANDOM
Rwork0.1742 ---
obs0.1753 31307 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 98.96 Å2 / Biso mean: 25.599 Å2 / Biso min: 13.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--1.55 Å2-0 Å2
3----1.58 Å2
Refinement stepCycle: final / Resolution: 1.55→44.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 0 28 141 1667
Biso mean--48.4 35.2 -
Num. residues----200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131606
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171526
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.6482183
X-RAY DIFFRACTIONr_angle_other_deg1.6021.5773542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.30122.22272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.99315263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5691510
X-RAY DIFFRACTIONr_chiral_restr0.0870.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021805
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02321
Refine LS restraints NCS

Ens-ID: 1 / Number: 3044 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.01

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 107 -
Rwork0.239 2175 -
all-2282 -
obs--94.34 %

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