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- PDB-2ze5: Crystal Structure of adenosine phosphate-isopentenyltransferase -

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Basic information

Entry
Database: PDB / ID: 2ze5
TitleCrystal Structure of adenosine phosphate-isopentenyltransferase
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Adenylate dimethylallyltransferase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 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 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 / 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 / _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)29,2253
Polymers28,8431
Non-polymers3832
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.392, 96.392, 65.197
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-447-

HOH

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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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.63 Å3/Da / Density % sol: 53.15 %
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, 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: 0.9792 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jan 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.31→68.2 Å / Num. obs: 13741 / % possible obs: 97.9 % / Biso Wilson estimate: 42.545 Å2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→68.2 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.077 / SU ML: 0.166 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25433 682 5 %RANDOM
Rwork0.20098 ---
obs0.2035 13059 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.708 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å20 Å2
2--2.08 Å20 Å2
3----4.16 Å2
Refinement stepCycle: LAST / Resolution: 2.31→68.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1824 0 24 46 1894
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0211890
X-RAY DIFFRACTIONr_angle_refined_deg2.2581.9772564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6385226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.40422.90393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.25215324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0641521
X-RAY DIFFRACTIONr_chiral_restr0.1370.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021445
X-RAY DIFFRACTIONr_nbd_refined0.2170.2841
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21273
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.285
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.25
X-RAY DIFFRACTIONr_mcbond_it1.191.51193
X-RAY DIFFRACTIONr_mcangle_it1.85521820
X-RAY DIFFRACTIONr_scbond_it3.2433840
X-RAY DIFFRACTIONr_scangle_it4.7534.5744
LS refinement shellResolution: 2.308→2.368 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 42 -
Rwork0.227 896 -
obs--91.87 %
Refinement TLS params.Method: refined / Origin x: 66.962 Å / Origin y: 57.6773 Å / Origin z: 18.0742 Å
111213212223313233
T0.005 Å2-0.0609 Å20.0553 Å2--0.1912 Å2-0.0206 Å2---0.1151 Å2
L1.6583 °2-1.0748 °2-0.8651 °2-3.1512 °20.6179 °2--1.6541 °2
S0.1167 Å °0.1728 Å °0.0822 Å °-0.3519 Å °-0.002 Å °-0.2966 Å °0.0658 Å °-0.2005 Å °-0.1147 Å °

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