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- PDB-3cbf: Crystal structure of LysN, alpha-aminoadipate aminotransferase, f... -

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Basic information

Entry
Database: PDB / ID: 3cbf
TitleCrystal structure of LysN, alpha-aminoadipate aminotransferase, from Thermus thermophilus HB27
ComponentsAlpha-aminodipate aminotransferase
KeywordsTRANSFERASE / alpha-aminoadipate aminotransferase / Thermus thermophilus / substrate specifity
Function / homology
Function and homology information


2-aminoadipate transaminase / 2-aminoadipate transaminase activity / 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
Chem-N5F / 2-aminoadipate transaminase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsTomita, T. / Miyazaki, T. / Miyagawa, T. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M.
Citation
Journal: Proteins / Year: 2008
Title: Mechanism for multiple-substrates recognition of alpha-aminoadipate aminotransferase from Thermus thermophilus
Authors: Tomita, T. / Miyagawa, T. / Miyazaki, T. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M.
#1: Journal: MICROBIOLOGY (READING, ENGL.) / Year: 2004
Title: alpha-aminoadipate aminotransferase from an extreme thermophilic bacterium, Thermus thermophilus
Authors: Miyazaki, T. / Miyazaki, J. / Yamane, H. / Nishiyama, M.
History
DepositionFeb 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Alpha-aminodipate aminotransferase
B: Alpha-aminodipate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5844
Polymers87,7992
Non-polymers7852
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-35 kcal/mol
Surface area26960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.279, 93.243, 150.880
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 Alpha-aminodipate aminotransferase


Mass: 43899.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: lysN / 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-N5F / (2S)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]hexanedioic acid


Mass: 392.298 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H21N2O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 18% PEG3350, 0.2M potassium fluoride, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 9, 2008 / 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: 1.67→50 Å / Num. all: 91233 / Num. obs: 91233 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 30.1
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.556 / Num. unique all: 8322 / Rsym value: 0.556 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z1Y

2z1y


Resolution: 1.67→34.69 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.448 / SU ML: 0.083 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELYHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24709 4415 5 %RANDOM
Rwork0.20191 ---
all0.20415 83725 --
obs0.20415 83725 96.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.772 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.67→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6156 0 52 431 6639
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226350
X-RAY DIFFRACTIONr_angle_refined_deg1.4912.0078598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6415800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50722.437279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.109151093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8351568
X-RAY DIFFRACTIONr_chiral_restr0.0980.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024856
X-RAY DIFFRACTIONr_nbd_refined0.2050.23353
X-RAY DIFFRACTIONr_nbtor_refined0.3080.24342
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2428
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.219
X-RAY DIFFRACTIONr_mcbond_it0.8541.54051
X-RAY DIFFRACTIONr_mcangle_it1.35926281
X-RAY DIFFRACTIONr_scbond_it2.21232584
X-RAY DIFFRACTIONr_scangle_it3.5294.52308
LS refinement shellResolution: 1.671→1.714 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 299 -
Rwork0.301 5766 -
obs--91.91 %

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