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- PDB-2ze8: Crystal Structure of adenosine phosphate-isopentenyltransferase c... -

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Basic information

Entry
Database: PDB / ID: 2ze8
TitleCrystal Structure of adenosine phosphate-isopentenyltransferase complexed with diphosphate
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
PYROPHOSPHATE 2- / Adenylate dimethylallyltransferase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 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 / Refinement description / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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: Isopentenyl transferase
B: Isopentenyl transferase
C: Isopentenyl transferase
D: Isopentenyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,0758
Polymers115,3714
Non-polymers7044
Water00
1
A: Isopentenyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0192
Polymers28,8431
Non-polymers1761
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Isopentenyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0192
Polymers28,8431
Non-polymers1761
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Isopentenyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0192
Polymers28,8431
Non-polymers1761
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Isopentenyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0192
Polymers28,8431
Non-polymers1761
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.510, 97.568, 131.108
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETASPASP1AA1 - 1481 - 148
21METMETASPASP1BB1 - 1481 - 148
31METMETASPASP1CC1 - 1481 - 148
41METMETASPASP1DD1 - 1481 - 148
52PROPROPROPRO4AA150 - 226150 - 226
62PROPROPROPRO4BB150 - 226150 - 226
72PROPROPROPRO4CC150 - 226150 - 226
82PROPROPROPRO4DD150 - 226150 - 226

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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.: 4
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-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2

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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: 2.7 Å3/Da / Density % sol: 54.49 %
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 diphosphate, 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: Jan 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→131.31 Å / Num. obs: 29244 / % possible obs: 97.83 % / Biso Wilson estimate: 39.384 Å2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→131.31 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.904 / SU B: 51.308 / SU ML: 0.431 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 7.289 / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30218 1566 5.1 %RANDOM
Rwork0.2303 ---
obs0.23385 29244 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.639 Å2
Baniso -1Baniso -2Baniso -3
1-3.88 Å20 Å20 Å2
2--4.1 Å20 Å2
3----7.98 Å2
Refinement stepCycle: LAST / Resolution: 2.8→131.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7260 0 36 0 7296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0217456
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9751.96710108
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8535900
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.18622.826368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.088151288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8051584
X-RAY DIFFRACTIONr_chiral_restr0.1690.21084
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025704
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3370.34321
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3770.55108
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2720.5574
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3750.332
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3680.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.14824631
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.88437272
X-RAY DIFFRACTIONr_scbond_it1.1523216
X-RAY DIFFRACTIONr_scangle_it1.81832836
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1174tight positional0.090.05
2B1174tight positional0.10.05
3C1174tight positional0.080.05
4D1174tight positional0.080.05
1A630medium positional0.30.5
2B630medium positional0.340.5
3C630medium positional0.350.5
4D630medium positional0.350.5
1A1174tight thermal0.20.5
2B1174tight thermal0.190.5
3C1174tight thermal0.180.5
4D1174tight thermal0.170.5
1A630medium thermal0.742
2B630medium thermal0.72
3C630medium thermal0.972
4D630medium thermal0.862
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 113 -
Rwork0.398 1966 -
obs--90.51 %
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)
15.48851.5753-1.95052.4806-1.23252.30550.11120.39850.269-0.38110.08890.10550.34070.2841-0.2001-0.09990.21050.0344-0.09040.2454-0.321139.307519.215767.4344
24.57981.66261.08473.45991.27693.18390.12560.7497-0.3792-0.76720.0904-0.0794-0.4002-0.0935-0.2160.14720.2328-0.0683-0.12720.1869-0.301959.2371-19.51611.8854
32.68621.2847-1.75354.4646-1.16952.90840.0432-0.69880.07780.41920.11680.37170.17680.6019-0.16-0.06180.22740.0205-0.06610.3048-0.312329.84069.876696.3467
43.30511.71971.06375.54041.86232.5550.1322-0.56130.01960.53720.037-0.31750.1131-0.2165-0.1692-0.10780.1315-0.06610.23320.2165-0.372668.5583-9.994430.867
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 226
2X-RAY DIFFRACTION2B1 - 226
3X-RAY DIFFRACTION3C1 - 226
4X-RAY DIFFRACTION4D1 - 226

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