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- PDB-2z1y: Crystal structure of LysN, alpha-aminoadipate aminotransferase (c... -

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Entry
Database: PDB / ID: 2z1y
TitleCrystal structure of LysN, alpha-aminoadipate aminotransferase (complexed with N-(5'-phosphopyridoxyl)-L-leucine), from Thermus thermophilus HB27
Components2-aminoadipate transaminase
KeywordsTRANSFERASE / alpha-aminoadipate aminotransferase / thermus thermophilus / substrate specifity
Function / homology
Function and homology information


2-aminoadipate transaminase / 2-aminoadipate transaminase activity / L-lysine biosynthetic process via aminoadipic acid / pyridoxal phosphate binding
Similarity search - Function
: / 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 ...: / 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
LEUCINE / PYRIDOXAL-5'-PHOSPHATE / 2-aminoadipate transaminase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsTomita, T. / Miyazaki, T. / Miyagawa, T. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: To be Published
Title: Mechanism of broad substrate specificity of alpha-aminoadipate aminotransferase from Thermus thermophilus
Authors: Tomita, T. / Miyazaki, T. / Miyagawa, T. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M.
#1: Journal: Microbiology / Year: 2004
Title: alpha-Aminoadipate aminotransferase from an extremely thermophilic bacterium, Thermus thermophilus
Authors: Miyazaki, T. / Miyazaki, J. / Yamane, H. / Nishiyama, M.
History
DepositionMay 16, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Jan 29, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / diffrn / diffrn_detector / entity / entity_name_com / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_database_status / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_torsion / pdbx_xplor_file / refine / refine_analyze / refine_hist / refine_ls_restr / refine_ls_shell / reflns_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _diffrn.pdbx_serial_crystal_experiment / _diffrn_detector.type / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_seq_type / _pdbx_contact_author.fax / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_contact_author.name_salutation / _pdbx_database_status.SG_entry / _pdbx_initial_refinement_model.details / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.range_id_1 / _pdbx_struct_sheet_hbond.range_id_2 / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_free_error / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_all / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_data_cutoff_high_absF / _refine.pdbx_data_cutoff_low_absF / _refine.pdbx_isotropic_thermal_model / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine.solvent_model_param_bsol / _refine.solvent_model_param_ksol / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_R_free / _refine_ls_shell.percent_reflns_obs / _reflns_shell.number_unique_all / _reflns_shell.number_unique_obs / _software.name / _software.version / _struct.pdbx_CASP_flag / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.db_code / _struct_sheet.id / _struct_sheet.number_strands / _struct_sheet_order.range_id_1 / _struct_sheet_order.range_id_2 / _struct_sheet_order.sense / _struct_sheet_order.sheet_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Description: Model completeness
Details: Since the previously registered model did not include water molecules, a new model was constructed with water molecules added.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2-aminoadipate transaminase
B: 2-aminoadipate transaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5566
Polymers87,7992
Non-polymers7574
Water13,583754
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-48 kcal/mol
Surface area27120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.107, 62.229, 107.439
Angle α, β, γ (deg.)90.00, 116.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 2-aminoadipate transaminase / 2-aminoadipate aminotransferase / Alpha-aminoadipate aminotransferase / AAA-AT / AadAT


Mass: 43899.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: lysN, TT_C0043 / Plasmid: pET-LysN7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codon-plus(DE3) / References: UniProt: Q72LL6, 2-aminoadipate transaminase
#2: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 754 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18% PEG 4000, 0.1M Tris-HCl (pH 7.0), 0.2M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Apr 22, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 81957 / Num. obs: 81957 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 13.8
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 81720 / Rsym value: 0.323 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DTV

2dtv
PDB Unreleased entry


Resolution: 1.75→36.86 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.226 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 4188 5.1 %RANDOM
Rwork0.153 ---
obs0.155 77545 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.02 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→36.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6127 0 48 754 6929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0126327
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166225
X-RAY DIFFRACTIONr_angle_refined_deg2.1811.8758557
X-RAY DIFFRACTIONr_angle_other_deg0.7231.74314297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2215789
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.839568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.322101077
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027542
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021476
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_it1.7371.4663162
X-RAY DIFFRACTIONr_mcbond_other1.7371.4663162
X-RAY DIFFRACTIONr_mcangle_it2.3022.6293946
X-RAY DIFFRACTIONr_mcangle_other2.3022.6293947
X-RAY DIFFRACTIONr_scbond_it3.7011.9123165
X-RAY DIFFRACTIONr_scbond_other3.7011.9133162
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5743.2994611
X-RAY DIFFRACTIONr_long_range_B_refined6.65716.557274
X-RAY DIFFRACTIONr_long_range_B_other6.56815.097080
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 298 -
Rwork0.206 5674 -
obs--99.5 %

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