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- PDB-3aq4: Molecular insights into plant cell proliferation disturbance by A... -

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Basic information

Entry
Database: PDB / ID: 3aq4
TitleMolecular insights into plant cell proliferation disturbance by Agrobacterium protein 6b
ComponentsADP-ribosylation factor 1
KeywordsTOXIN / ADP-ribosylation factor / miRNA processing machineries / ADP-ribosylation
Function / homology
Function and homology information


response to brefeldin A / regulation of auxin metabolic process / vesicle-mediated transport to the plasma membrane / auxin-activated signaling pathway / phospholipase activator activity / vesicle-mediated transport / intracellular protein transport / trans-Golgi network / early endosome / GTP binding ...response to brefeldin A / regulation of auxin metabolic process / vesicle-mediated transport to the plasma membrane / auxin-activated signaling pathway / phospholipase activator activity / vesicle-mediated transport / intracellular protein transport / trans-Golgi network / early endosome / GTP binding / Golgi apparatus / cytoplasm / cytosol
Similarity search - Function
small GTPase Arf family profile. / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / ADP-ribosylation factor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_atom_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_atom_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.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_atom_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosylation factor 1
B: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7696
Polymers41,8342
Non-polymers9354
Water5,224290
1
A: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3843
Polymers20,9171
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3843
Polymers20,9171
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.710, 89.977, 46.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ADP-ribosylation factor 1 / AtARF1


Mass: 20916.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ARF1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36397
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG6000, magnesium chloride, HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→89.8 Å / Num. all: 33100 / Num. obs: 33083 / % possible obs: 99.69 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.8→1.85 Å / % possible all: 99.57

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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: 1.8→89.8 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.81 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24148 1750 5 %RANDOM
Rwork0.19858 ---
obs0.20076 33083 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.032 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2---0.21 Å20 Å2
3---1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→89.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2665 0 58 290 3013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222770
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9763753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0815329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56724.154130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52915491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4011519
X-RAY DIFFRACTIONr_chiral_restr0.0990.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022032
X-RAY DIFFRACTIONr_nbd_refined0.2090.21208
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21855
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2217
X-RAY DIFFRACTIONr_metal_ion_refined0.0320.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3420.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.216
X-RAY DIFFRACTIONr_mcbond_it1.0281.51692
X-RAY DIFFRACTIONr_mcangle_it1.61622642
X-RAY DIFFRACTIONr_scbond_it2.48231255
X-RAY DIFFRACTIONr_scangle_it3.8524.51111
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 129 -
Rwork0.218 2413 -
obs--99.57 %
Refinement TLS params.Method: refined / Origin x: 29.1465 Å / Origin y: 12.3102 Å / Origin z: 11.3442 Å
111213212223313233
T-0.1132 Å20.0059 Å20.014 Å2--0.107 Å2-0.034 Å2---0.1083 Å2
L1.6879 °21.4822 °2-0.6108 °2-1.8466 °2-0.6418 °2--0.4141 °2
S-0.1182 Å °0.1039 Å °-0.1576 Å °-0.161 Å °0.0718 Å °-0.1166 Å °0.0408 Å °0.0139 Å °0.0464 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 181
2X-RAY DIFFRACTION1B4 - 181

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