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- PDB-4b2g: Crystal Structure of an Indole-3-Acetic Acid Amido Synthase from ... -

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Basic information

Entry
Database: PDB / ID: 4b2g
TitleCrystal Structure of an Indole-3-Acetic Acid Amido Synthase from Vitis vinifera Involved in Auxin Homeostasis
ComponentsGH3-1 AUXIN CONJUGATING ENZYME
KeywordsSIGNALING PROTEIN / IGNALING PROTEIN / ADENYLATE / AMINO ACID CONJUGATION / PLANT GROWTH
Function / homology
Function and homology information


acid-amino acid ligase activity / cytoplasm
Similarity search - Function
: / : / GH3 family central domain / GH3 family C-terminal domain / GH3 family / GH3 family N-terminal domain
Similarity search - Domain/homology
MALONATE ION / Chem-V1N / Indole-3-acetic acid-amido synthetase GH3.1
Similarity search - Component
Biological speciesVITIS VINIFERA (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsPeat, T.S. / Bottcher, C. / Newman, J. / Lucent, D. / Cowieson, N. / Davies, C.
CitationJournal: Plant Cell / Year: 2012
Title: Crystal Structure of an Indole-3-Acetic Acid Amido Synthetase from Grapevine Involved in Auxin Homeostasis.
Authors: Peat, T.S. / Bottcher, C. / Newman, J. / Lucent, D. / Cowieson, N. / Davies, C.
History
DepositionJul 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: GH3-1 AUXIN CONJUGATING ENZYME
B: GH3-1 AUXIN CONJUGATING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,7238
Polymers137,3632
Non-polymers1,3616
Water2,702150
1
A: GH3-1 AUXIN CONJUGATING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3624
Polymers68,6811
Non-polymers6803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GH3-1 AUXIN CONJUGATING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3624
Polymers68,6811
Non-polymers6803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.167, 91.167, 338.065
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein GH3-1 AUXIN CONJUGATING ENZYME


Mass: 68681.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VITIS VINIFERA (wine grape) / Strain: CABERNET SAUVIGNON / Description: CABERNET SAUVIGNON FROM SOUTH AUSTRALIA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: F6H697
#2: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-V1N / [(2S,3R,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl] 2-(1H-indol-3-yl)ethyl hydrogen phosphate


Mass: 476.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H21N6O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMALONATE ION (MLI): USED AS A CRYSTALLIZATION REAGENT LIGAND V1N IS A SUBSTRATE MIMETIC INHIBITOR
Sequence detailsLAST 11 RESIDUES ARE PART OF A HIS-TAG ADDED TO THE PROTEIN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 53.5 %
Description: STRUCTURE WAS SOLVED INITIALLY WTH A SINGLE PT DERIVATIVE AND LATER REFINED TO HIGHER RESOLUTION, 2.40 A, USING A SECOND NATIVE DATA SET.
Crystal growTemperature: 293 K / pH: 7
Details: THE PROTEIN WAS CONCENTRATED TO 6 MG/ML IN THE PRESENCE OF 10 MM INHIBITOR AND CRYSTALLIZED AT 20 DEGREES CELSIUS IN 0.7 TO 1.0 M SODIUM MALONATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.37→338.07 Å / Num. obs: 59192 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 14.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 15.4
Reflection shellResolution: 2.37→2.5 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.903 / SU B: 8.794 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.407 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. DISORDERED REGIONS WERE NOT MODELLED UNLESS THERE WAS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. DISORDERED REGIONS WERE NOT MODELLED UNLESS THERE WAS SUFFICIENT DENSITY FOR AT LEAST THE BACKBONE
RfactorNum. reflection% reflectionSelection details
Rfree0.26387 2919 5.1 %RANDOM
Rwork0.22445 ---
obs0.22646 54126 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.482 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.26 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9004 0 94 150 9248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.029384
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.98612764
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50551161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9723.35409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.062151587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5011571
X-RAY DIFFRACTIONr_chiral_restr0.0760.21413
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217210
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 210 -
Rwork0.34 3508 -
obs--100 %

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