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- PDB-3ei9: Crystal structure of K270N variant of LL-diaminopimelate aminotra... -

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Basic information

Entry
Database: PDB / ID: 3ei9
TitleCrystal structure of K270N variant of LL-diaminopimelate aminotransferase from Arabidopsis thaliana complexed with L-Glu: External aldimine form
ComponentsLL-diaminopimelate aminotransferase
KeywordsTRANSFERASE / aminotransferase / lysine biosynthesis / Pyridoxal 5' phosphate / external aldimine / LL-diaminopimelate / Chloroplast / Pyridoxal phosphate / Transit peptide
Function / homology
Function and homology information


LL-diaminopimelate aminotransferase / L,L-diaminopimelate aminotransferase activity / systemic acquired resistance, salicylic acid mediated signaling pathway / transaminase activity / lysine biosynthetic process via diaminopimelate / chloroplast stroma / chloroplast / pyridoxal phosphate binding / copper ion binding / plasma membrane
Similarity search - Function
LL-diaminopimelate aminotransferase/aminotransferase ALD1 / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...LL-diaminopimelate aminotransferase/aminotransferase ALD1 / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PL6 / LL-diaminopimelate aminotransferase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsWatanabe, N. / Clay, M.D. / van Belkum, M.J. / Cherney, M.M. / Vederas, J.C. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Mechanism of substrate recognition and PLP-induced conformational changes in LL-diaminopimelate aminotransferase from Arabidopsis thaliana.
Authors: Watanabe, N. / Clay, M.D. / van Belkum, M.J. / Cherney, M.M. / Vederas, J.C. / James, M.N.
History
DepositionSep 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LL-diaminopimelate aminotransferase
B: LL-diaminopimelate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,59813
Polymers95,0052
Non-polymers1,59311
Water19,8351101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-40 kcal/mol
Surface area28910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.577, 102.577, 171.177
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein LL-diaminopimelate aminotransferase / LL-DAP-aminotransferase / DAP-aminotransferase / DAP-AT / AtDAP-AT / Protein ABERRANT GROWTH AND DEATH 2


Mass: 47502.570 Da / Num. of mol.: 2 / Fragment: UNP residues 36 to 461 / Mutation: K270N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: DAP, AGD2, At4g33680, T16L1.170 / Production host: Escherichia coli (E. coli)
References: UniProt: Q93ZN9, LL-diaminopimelate aminotransferase
#2: Chemical ChemComp-PL6 / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-glutamic acid


Mass: 376.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H17N2O9P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1101 / 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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 45% (NH4)2SO4, 0.1 M HEPES pH 7.5, 3% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115872 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2007
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115872 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. all: 151099 / Num. obs: 151099 / % possible obs: 99.9 % / Rsym value: 0.082
Reflection shellResolution: 1.55→1.61 Å / Rsym value: 0.443 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Z20

2z20


Resolution: 1.55→39.44 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.067 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.067 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19052 7585 5 %RANDOM
Rwork0.16394 ---
obs0.16524 143441 99.89 %-
all-143441 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.451 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.2 Å20 Å2
2---0.4 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.55→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6346 0 101 1101 7548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226594
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.9588932
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2935820
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30924.014294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.483151032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.31532
X-RAY DIFFRACTIONr_chiral_restr0.0820.2963
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025068
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.23372
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.24634
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2851
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.249
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7161.54152
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16926566
X-RAY DIFFRACTIONr_scbond_it1.94632740
X-RAY DIFFRACTIONr_scangle_it3.044.52366
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 534 -
Rwork0.235 10437 -
obs--99.72 %

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