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- PDB-2zp7: Crystal structure of LysN, alpha-aminoadipate aminotransferase (L... -

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Basic information

Entry
Database: PDB / ID: 2zp7
TitleCrystal structure of LysN, alpha-aminoadipate aminotransferase (Leucine complex), from Thermus thermophilus HB27
ComponentsAlpha-aminodipate aminotransferase
KeywordsTRANSFERASE / alpha-aminoadipate aminotransferase / PLP-Leucine complex / Aminotransferase
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
LEUCINE / PYRIDOXAL-5'-PHOSPHATE / 2-aminoadipate transaminase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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 / Year: 2004
Title: alpha-Aminoadipate aminotransferase from an extremely thermophilic bacterium, Thermus thermophilus
Authors: Miyazaki, T. / Miyazaki, J. / Yamane, H. / Nishiyama, M.
History
DepositionJun 30, 2008Deposition site: PDBJ / Processing site: PDBJ
SupersessionJan 13, 2009ID: 2ZG5
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-aminodipate aminotransferase
B: Alpha-aminodipate aminotransferase
C: Alpha-aminodipate aminotransferase
D: Alpha-aminodipate aminotransferase
E: Alpha-aminodipate aminotransferase
F: Alpha-aminodipate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,27515
Polymers263,3986
Non-polymers1,8769
Water9,998555
1
A: Alpha-aminodipate aminotransferase
C: Alpha-aminodipate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4255
Polymers87,7992
Non-polymers6253
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-40 kcal/mol
Surface area27160 Å2
MethodPISA
2
B: Alpha-aminodipate aminotransferase
D: Alpha-aminodipate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4255
Polymers87,7992
Non-polymers6253
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-43 kcal/mol
Surface area26900 Å2
MethodPISA
3
E: Alpha-aminodipate aminotransferase
F: Alpha-aminodipate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4255
Polymers87,7992
Non-polymers6253
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-39 kcal/mol
Surface area27210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.948, 167.639, 119.358
Angle α, β, γ (deg.)90.00, 97.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alpha-aminodipate aminotransferase


Mass: 43899.738 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: lysN / Plasmid: pET-26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RILCodonPlus(DE3) / References: UniProt: Q72LL6, 2-aminoadipate transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 19, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. all: 101430 / Num. obs: 101430 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 19.4
Reflection shellResolution: 2.26→2.34 Å / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 4.3

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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 / Resolution: 2.26→41.92 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.82 / SU ML: 0.175 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.455 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26292 5030 5 %RANDOM
Rwork0.20462 ---
obs0.20753 95673 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.26→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18198 0 117 555 18870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02218696
X-RAY DIFFRACTIONr_angle_refined_deg1.4992.00525296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16452340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20522.574816
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.528153162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.63815192
X-RAY DIFFRACTIONr_chiral_restr0.0980.22742
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214280
X-RAY DIFFRACTIONr_nbd_refined0.2160.29695
X-RAY DIFFRACTIONr_nbtor_refined0.3070.212529
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.21023
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.2185
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.229
X-RAY DIFFRACTIONr_mcbond_it0.7461.511998
X-RAY DIFFRACTIONr_mcangle_it1.236218579
X-RAY DIFFRACTIONr_scbond_it1.91537504
X-RAY DIFFRACTIONr_scangle_it3.1334.56717
LS refinement shellResolution: 2.26→2.318 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 366 -
Rwork0.193 6862 -
obs--97.05 %

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