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

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Basic information

Entry
Database: PDB / ID: 3eib
TitleCrystal structure of K270N variant of LL-diaminopimelate aminotransferase from Arabidopsis thaliana
ComponentsLL-diaminopimelate aminotransferase
KeywordsTRANSFERASE / aminotransferase / lysine biosynthesis / Pyridoxal 5' phosphate / Arabidopsis thaliana / 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
PYRIDOXAL-5'-PHOSPHATE / LL-diaminopimelate aminotransferase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)96,07210
Polymers95,0052
Non-polymers1,0678
Water18,3031016
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-39 kcal/mol
Surface area29030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.045, 103.045, 171.984
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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1016 / 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: 2.77 Å3/Da / Density % sol: 55.67 %
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: SSRL / Beamline: BL7-1 / Wavelength: 0.976067 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2008
RadiationMonochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976067 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. all: 83053 / Num. obs: 83053 / % possible obs: 91.4 % / Rsym value: 0.062
Reflection shellResolution: 1.85→1.92 Å / Num. unique all: 8069 / Rsym value: 0.687 / % possible all: 89.9

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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: 1.85→39.59 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.455 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19749 4158 5 %RANDOM
Rwork0.16225 ---
obs0.16401 78837 91.35 %-
all-78837 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å2-0.35 Å20 Å2
2---0.7 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6356 0 63 1016 7435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226570
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9538910
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6855821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96124295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.338151033
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6651532
X-RAY DIFFRACTIONr_chiral_restr0.0960.2958
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025054
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.23163
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24524
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2755
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8151.54195
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2726556
X-RAY DIFFRACTIONr_scbond_it2.18132726
X-RAY DIFFRACTIONr_scangle_it3.4364.52354
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 287 -
Rwork0.226 5673 -
obs--89.77 %

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