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- PDB-4l39: Crystal structure of GH3.12 from Arabidopsis thaliana in complex ... -

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Basic information

Entry
Database: PDB / ID: 4l39
TitleCrystal structure of GH3.12 from Arabidopsis thaliana in complex with AMPCPP and salicylate
Components4-substituted benzoates-glutamate ligase GH3.12
KeywordsLIGASE / acyl acid amido synthase / protein-ligand complex / magnesium
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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / 2-HYDROXYBENZOIC ACID / 4-substituted benzoates-glutamate ligase GH3.12
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsZubieta, C. / Jez, J.M. / Brown, E. / Marcellin, R. / Kapp, U. / Round, A. / Westfall, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Determination of the GH3.12 protein conformation through HPLC-integrated SAXS measurements combined with X-ray crystallography.
Authors: Round, A. / Brown, E. / Marcellin, R. / Kapp, U. / Westfall, C.S. / Jez, J.M. / Zubieta, C.
History
DepositionJun 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Sep 20, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)132,8367
Polymers131,5252
Non-polymers1,3115
Water3,837213
1
A: 4-substituted benzoates-glutamate ligase GH3.12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4304
Polymers65,7621
Non-polymers6683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 4-substituted benzoates-glutamate ligase GH3.12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4063
Polymers65,7621
Non-polymers6432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.360, 114.088, 157.976
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 4-substituted benzoates-glutamate ligase GH3.12 / GH3.12 acyl acid amido synthetase / Auxin-responsive GH3-like protein 12 / AtGH3-12 / Protein GH3- ...GH3.12 acyl acid amido synthetase / 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.: 2
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
Production host: Escherichia coli (E. coli)
References: UniProt: Q9LYU4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#4: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.16 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG3350, 0.25 M ammonium acetate, 0.1 M sodium acetate, 5 mM TCEP, 5 mM salicylate, 5 mM AMPCPP, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 4, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.81→92.49 Å / Num. all: 28243 / Num. obs: 28172 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.26 / Rsym value: 0.26 / Net I/σ(I): 8
Reflection shellResolution: 2.81→3 Å / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.73 / % possible all: 99.5

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Processing

Software
NameVersionClassification
EDNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EPM

4epm


Resolution: 2.81→58.004 Å / SU ML: 0.39 / σ(F): 1.35 / Phase error: 29.17 / Stereochemistry target values: ML
Details: RESIDUES FOR THE C-TERMINAL DOMAIN (430-575) WERE MODELED BASED ON PDB ENTRY 4EPM. THESE RESIDUES EXHIBITED HIGH B-FACTORS AND POOR SIDECHAIN AND MAIN CHAIN DENSITY.
RfactorNum. reflection% reflection
Rfree0.2666 1418 5.03 %
Rwork0.1979 --
obs0.2014 28170 99.75 %
all-28243 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.81→58.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8316 0 83 213 8612
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0178630
X-RAY DIFFRACTIONf_angle_d1.54711749
X-RAY DIFFRACTIONf_dihedral_angle_d15.8633120
X-RAY DIFFRACTIONf_chiral_restr0.0861337
X-RAY DIFFRACTIONf_plane_restr0.0071506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8101-2.91050.361450.27262608X-RAY DIFFRACTION99
2.9105-3.02710.37751460.23212626X-RAY DIFFRACTION100
3.0271-3.16480.31521150.21032666X-RAY DIFFRACTION100
3.1648-3.33170.28081110.21492655X-RAY DIFFRACTION100
3.3317-3.54040.28671280.22492667X-RAY DIFFRACTION100
3.5404-3.81370.28841580.18212632X-RAY DIFFRACTION100
3.8137-4.19740.21821300.15182692X-RAY DIFFRACTION100
4.1974-4.80450.21041860.14432641X-RAY DIFFRACTION100
4.8045-6.05210.21351460.18272712X-RAY DIFFRACTION100
6.0521-58.01660.2741530.23212853X-RAY DIFFRACTION100

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