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- PDB-4epm: Crystal Structure of Arabidopsis GH3.12 (PBS3) in Complex with AMP -

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Basic information

Entry
Database: PDB / ID: 4epm
TitleCrystal Structure of Arabidopsis GH3.12 (PBS3) in Complex with AMP
Components4-substituted benzoates-glutamate ligase GH3.12
KeywordsLIGASE / ANL Superfamily / Acyl acid-amido synthetase / Adenylation
Function / homology
Function and homology information


N-(4-aminobenzoyl)-L-glutamate synthetase activity / N-benzoyl-L-glutamate synthetase activity / N-vanillate-L-glutamate synthetase activity / N-(4-hydroxybenzoyl)-L-glutamate synthetase activity / positive regulation of plant-type hypersensitive response / benzoate metabolic process / salicylic acid mediated signaling pathway / regulation of systemic acquired resistance / detection of fungus / plant-type hypersensitive response ...N-(4-aminobenzoyl)-L-glutamate synthetase activity / N-benzoyl-L-glutamate synthetase activity / N-vanillate-L-glutamate synthetase activity / N-(4-hydroxybenzoyl)-L-glutamate synthetase activity / positive regulation of plant-type hypersensitive response / benzoate metabolic process / salicylic acid mediated signaling pathway / regulation of systemic acquired resistance / detection of fungus / plant-type hypersensitive response / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / defense response / cellular response to hypoxia / defense response to bacterium
Similarity search - Function
: / : / GH3 family central domain / GH3 family C-terminal domain / GH3 family / GH3 family N-terminal domain
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 4-substituted benzoates-glutamate ligase GH3.12
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsWestfall, C.S. / Zubieta, C. / Herrmann, J. / Kapp, U. / Nanao, M.H. / Jez, J.M.
CitationJournal: Science / Year: 2012
Title: Structural basis for prereceptor modulation of plant hormones by GH3 proteins.
Authors: Westfall, C.S. / Zubieta, C. / Herrmann, J. / Kapp, U. / Nanao, M.H. / Jez, J.M.
History
DepositionApr 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Feb 28, 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: 4-substituted benzoates-glutamate ligase GH3.12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2063
Polymers65,7621
Non-polymers4432
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 4-substituted benzoates-glutamate ligase GH3.12
hetero molecules

A: 4-substituted benzoates-glutamate ligase GH3.12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,4116
Polymers131,5252
Non-polymers8874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area5170 Å2
ΔGint-51 kcal/mol
Surface area43720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.765, 65.769, 154.972
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-878-

HOH

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Components

#1: Protein 4-substituted benzoates-glutamate ligase GH3.12 / Auxin-responsive GH3-like protein 12 / AtGH3-12 / Protein GH3-LIKE DEFENSE GENE 1 / Protein ...Auxin-responsive GH3-like protein 12 / AtGH3-12 / Protein GH3-LIKE DEFENSE GENE 1 / Protein GRETCHEN HAGEN 3.12 / Protein HOPW1-1-INTERACTING 3 / Protein avrPPHB SUSCEPTIBLE 3


Mass: 65762.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress)
Gene: GH3.12, GDG1, PBS3, WIN3, At5g13320, T22N19.5, T31B5.140
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q9LYU4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 M Ammonium Sulfate, .1 M PIPES, 2% PEG-400, 5 mM AMP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2011
RadiationMonochromator: SI(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→42.5 Å / Num. all: 36545 / Num. obs: 35574 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Net I/σ(I): 13.2
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 1722 / % possible all: 95.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.099→42.532 Å / Occupancy max: 1 / Occupancy min: 0.24 / SU ML: 0.26 / σ(F): 0 / Phase error: 23.67 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 1785 5.02 %Random
Rwork0.1996 33789 --
obs0.2017 35574 97.31 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.72 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 118.36 Å2 / Biso mean: 32.2026 Å2 / Biso min: 7.72 Å2
Baniso -1Baniso -2Baniso -3
1-12.5603 Å2-0 Å2-0 Å2
2---4.8281 Å20 Å2
3----7.7323 Å2
Refinement stepCycle: LAST / Resolution: 2.099→42.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4410 0 28 255 4693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074573
X-RAY DIFFRACTIONf_angle_d1.0366212
X-RAY DIFFRACTIONf_chiral_restr0.068700
X-RAY DIFFRACTIONf_plane_restr0.004793
X-RAY DIFFRACTIONf_dihedral_angle_d13.3551705
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0989-2.17390.32271680.25953226339495
2.1739-2.26090.27091970.22213292348997
2.2609-2.36380.25271650.20673362352798
2.3638-2.48850.25791830.20193370355398
2.4885-2.64430.22191530.19783357351097
2.6443-2.84850.27171910.20673381357298
2.8485-3.1350.2641700.20123403357398
3.135-3.58850.23911740.18753415358998
3.5885-4.52030.18951970.16813438363598
4.5203-42.54120.23751870.21323545373296
Refinement TLS params.Method: refined / Origin x: -26.9084 Å / Origin y: 28.4883 Å / Origin z: -21.2451 Å
111213212223313233
T0.1152 Å2-0.0269 Å20.0067 Å2-0.0816 Å2-0.0031 Å2--0.092 Å2
L0.2019 °2-0.0683 °20.0387 °2-0.3057 °20.0203 °2--0.4055 °2
S0.0212 Å °0.0683 Å °0.0034 Å °-0.0677 Å °0.0192 Å °0.0182 Å °0.0155 Å °-0.038 Å °-0.0325 Å °
Refinement TLS groupSelection details: chain A

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