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- PDB-3aq2: Molecular insights into plant cell proliferation disturbance by A... -

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Basic information

Entry
Database: PDB / ID: 3aq2
TitleMolecular insights into plant cell proliferation disturbance by Agrobacterium protein 6b
Components6b protein
KeywordsTOXIN / miRNA machineries / ADP-ribosylation fold
Function / homologyCytokinin glycosidase / RolB/RolC glucosidase family / 6b protein
Function and homology information
Biological speciesAgrobacterium vitis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWang, M.M. / Yuan, Y.A.
CitationJournal: Genes Dev. / Year: 2011
Title: Molecular insights into plant cell proliferation disturbance by Agrobacterium protein 6b
Authors: Wang, M.M. / Soyano, T. / Machida, S. / Yang, J.Y. / Jung, C. / Chua, N.H. / Yuan, Y.A.
History
DepositionOct 25, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6b protein
B: 6b protein


Theoretical massNumber of molelcules
Total (without water)47,5392
Polymers47,5392
Non-polymers00
Water6,161342
1
A: 6b protein


Theoretical massNumber of molelcules
Total (without water)23,7691
Polymers23,7691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 6b protein


Theoretical massNumber of molelcules
Total (without water)23,7691
Polymers23,7691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.366, 89.926, 59.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-297-

HOH

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Components

#1: Protein 6b protein


Mass: 23769.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium vitis (bacteria) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q44522
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: ammonium dehydrate phosphate, sodium citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.65→79.31 Å / Num. all: 49400 / Num. obs: 49396 / % possible obs: 99.79 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.649→1.692 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→79.31 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.07 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20557 2659 5.1 %RANDOM
Rwork0.1784 ---
obs0.17978 49396 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.334 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å20 Å2
2--0.28 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.65→79.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 0 342 3388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213117
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.9454236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2165372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59322.97165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13515500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8651532
X-RAY DIFFRACTIONr_chiral_restr0.0790.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022436
X-RAY DIFFRACTIONr_nbd_refined0.1920.21428
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22160
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.090.2246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.247
X-RAY DIFFRACTIONr_mcbond_it0.6651.51913
X-RAY DIFFRACTIONr_mcangle_it1.09123018
X-RAY DIFFRACTIONr_scbond_it1.77231368
X-RAY DIFFRACTIONr_scangle_it2.74.51218
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 194 -
Rwork0.229 3561 -
obs--98.04 %
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)
11.1187-0.42340.35281.2793-0.22720.68340.00620.02050.00760.0722-0.0348-0.1010.03350.05350.0286-0.06140.00190-0.06930.0076-0.080817.7852-18.8768-6.7796
21.38670.09980.01081.03920.32751.33720.0439-0.09350.01250.0417-0.07660.02980.0389-0.03240.0327-0.0531-0.00820.0176-0.0215-0.0154-0.0530.1189-30.0819-31.1289
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 204
2X-RAY DIFFRACTION2B6 - 204

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