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- PDB-2ze6: Crystal Structure of adenosine phosphate-isopentenyltransferase c... -

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Basic information

Entry
Database: PDB / ID: 2ze6
TitleCrystal Structure of adenosine phosphate-isopentenyltransferase complexed with substrate analog, DMASPP
ComponentsIsopentenyl transferase
KeywordsTRANSFERASE / Crown gall tumor / Cytokinin biosynthesis
Function / homology
Function and homology information


adenylate dimethylallyltransferase (AMP-dependent) / AMP dimethylallyltransferase activity / cytokinin biosynthetic process
Similarity search - Function
Adenylate dimethylallyltransferase / Isopentenyl transferase / Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain / Helix Hairpins / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / DIMETHYLALLYL S-THIOLODIPHOSPHATE / Adenylate dimethylallyltransferase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsSakakibara, H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural insight into the reaction mechanism and evolution of cytokinin biosynthesis.
Authors: Sugawara, H. / Ueda, N. / Kojima, M. / Makita, N. / Yamaya, T. / Sakakibara, H.
History
DepositionDec 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Oct 16, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Isopentenyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4523
Polymers28,8431
Non-polymers6092
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.417, 96.417, 65.068
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Isopentenyl transferase / adenosine phosphate-isopentenyl transferase / Dimethylallyl transferase / Trans-zeatin producing protein


Mass: 28842.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: tzs / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: P58758, adenylate dimethylallyltransferase (AMP-dependent)
#2: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate / Dimethylallyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 1.4-2.0M sodium formate, 5mM magnesium chloride, 0.1M sodium acetate buffer, 20mM dimethylallyl S-thiolodiphosphate, pH 4.8-5.4., VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→68.2 Å / Num. obs: 17222 / % possible obs: 98.29 % / Biso Wilson estimate: 24.01 Å2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→68.2 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 13.887 / SU ML: 0.176 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26424 934 5.1 %RANDOM
Rwork0.19633 ---
obs0.19957 17222 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.277 Å2
Baniso -1Baniso -2Baniso -3
1-3.08 Å20 Å20 Å2
2--3.08 Å20 Å2
3----6.17 Å2
Refinement stepCycle: LAST / Resolution: 2.1→68.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 37 38 1899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0211903
X-RAY DIFFRACTIONr_angle_refined_deg2.6051.9852583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0285226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32322.90393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.52315324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6421521
X-RAY DIFFRACTIONr_chiral_restr0.1530.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021450
X-RAY DIFFRACTIONr_nbd_refined0.2390.2852
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21294
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.268
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2740.25
X-RAY DIFFRACTIONr_mcbond_it1.3731.51183
X-RAY DIFFRACTIONr_mcangle_it2.11221820
X-RAY DIFFRACTIONr_scbond_it3.6153849
X-RAY DIFFRACTIONr_scangle_it5.1244.5763
LS refinement shellResolution: 2.099→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 69 -
Rwork0.25 1113 -
obs--89.68 %
Refinement TLS params.Method: refined / Origin x: 67.0448 Å / Origin y: 57.5566 Å / Origin z: 18.0177 Å
111213212223313233
T0.0869 Å2-0.1182 Å20.0798 Å2--0.2665 Å2-0.0136 Å2---0.1706 Å2
L2.1428 °2-1.3967 °2-1.2669 °2-4.3017 °21.1964 °2--2.8184 °2
S0.1926 Å °0.1958 Å °0.0692 Å °-0.7072 Å °0.0098 Å °-0.3584 Å °-0.0295 Å °-0.231 Å °-0.2024 Å °

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