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- PDB-4fl0: Crystal structure of ALD1 from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 4fl0
TitleCrystal structure of ALD1 from Arabidopsis thaliana
ComponentsAminotransferase ALD1
KeywordsTRANSFERASE / Structural Genomics / Protein Structure Initiative / Israel Structural Proteomics Center / ISPC / sandwich fold and architecture / pathogen resistance / PLP Nbinding
Function / homology
Function and homology information


L-lysine alpha-aminotransferase / L-pipecolic acid biosynthetic process / systemic acquired resistance / systemic acquired resistance, salicylic acid mediated signaling pathway / leaf senescence / Transferases; Transferring nitrogenous groups; Transaminases / plastid / transaminase activity / chloroplast / pyridoxal phosphate binding / defense response to bacterium
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 / Aminotransferase ALD1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSobolev, V. / Edelman, M. / Dym, O. / Unger, T. / Albeck, S. / Kirma, M. / Galili, G. / Israel Structural Proteomics Center (ISPC)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of ALD1, a plant-specific homologue of the universal diaminopimelate aminotransferase enzyme of lysine biosynthesis.
Authors: Sobolev, V. / Edelman, M. / Dym, O. / Unger, T. / Albeck, S. / Kirma, M. / Galili, G.
History
DepositionJun 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase ALD1
B: Aminotransferase ALD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7654
Polymers101,2702
Non-polymers4942
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-29 kcal/mol
Surface area29470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.280, 89.870, 180.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 35 - 439 / Label seq-ID: 35 - 439

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Aminotransferase ALD1 / AGD2-like defense response protein 1


Mass: 50635.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ALD1, At2g13810, F13J11.16 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9ZQI7, Transferases; Transferring nitrogenous groups; Transaminases
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 5.5
Details: 100 mM sodium citrate tribasic dihydrate, 2.2mM FOS-Choline -8 fluorinated, and 18% polyethylene glycol 3,350, pH 5.5, Microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 55617 / Num. obs: 54171 / % possible obs: 7.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.14 Å / % possible all: 83.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.42 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.44 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.317 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24097 2136 5.1 %RANDOM
Rwork0.20532 ---
obs0.20708 40152 99.88 %-
all-52618 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0 Å2-0 Å2
2--4.48 Å20 Å2
3----4.72 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6323 0 32 13 6368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0196508
X-RAY DIFFRACTIONr_bond_other_d0.0050.026038
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.958835
X-RAY DIFFRACTIONr_angle_other_deg1.094313863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5525813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12324.013299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81151030
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0861534
X-RAY DIFFRACTIONr_chiral_restr0.1050.2967
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217495
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021575
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_it1.0311.54028
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.82126489
X-RAY DIFFRACTIONr_scbond_it3.08632415
X-RAY DIFFRACTIONr_scangle_it4.7474.52273
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23431 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 190 -
Rwork0.271 2847 -
obs--99.54 %

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