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- PDB-2egy: Crystal structure of LysN, alpha-aminoadipate aminotransferase (s... -

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Basic information

Entry
Database: PDB / ID: 2egy
TitleCrystal structure of LysN, alpha-aminoadipate aminotransferase (substrate free form), from Thermus thermophilus HB27
ComponentsAlpha-aminodipate aminotransferase
KeywordsTRANSFERASE / alpha-aminoadipate aminotransferase / thermus thermophilus / substrate specificity
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 / Alpha-Beta Complex ...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 / 2-aminoadipate transaminase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsTomita, T. / Miyazaki, T. / Miyagawa, T. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M.
Citation
Journal: To be Published
Title: Crystal structure of LysN, alpha-aminoadipate aminotransferase, from Thermus thermophilus HB27
Authors: Tomita, T. / Miyazaki, T. / Miyagawa, T. / Fushinobu, S. / Kuzuyama, T. / Nishiyama, M.
#1: Journal: MICROBIOLOGY (READING, ENGL.) / Year: 2004
Title: alpha-Aminoadipate aminotransferase from an extremely thermophilic bacterium, Thermus thermophilus
Authors: Miyazaki, T. / Miyazaki, J. / Yamane, H. / Nishiyama, M.
History
DepositionMar 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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.ptnr1_label_seq_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_conn.ptnr2_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: Alpha-aminodipate aminotransferase
B: Alpha-aminodipate aminotransferase
C: Alpha-aminodipate aminotransferase
D: Alpha-aminodipate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,5888
Polymers175,5994
Non-polymers9894
Water1,49583
1
A: Alpha-aminodipate aminotransferase
B: Alpha-aminodipate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2944
Polymers87,7992
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-42 kcal/mol
Surface area27660 Å2
MethodPISA, PQS
2
C: Alpha-aminodipate aminotransferase
D: Alpha-aminodipate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,2944
Polymers87,7992
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-42 kcal/mol
Surface area27980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.415, 138.510, 111.745
Angle α, β, γ (deg.)90.00, 100.21, 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.: 4
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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 17% PEG 4000, 0.1M tri-Sodium Citrate (pH6.6), 0.2M Ammonium Sulfate, 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 QUAMTUM 4r / Detector: CCD / Date: Dec 17, 2006 / 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: 2.67→50 Å / Num. all: 48044 / Num. obs: 48044 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062
Reflection shellResolution: 2.67→2.67 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 4.3 / Num. unique all: 4516 / Rsym value: 0.232

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DTV

2dtv
PDB Unreleased entry


Resolution: 2.67→43.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2775934.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2357 5 %RANDOM
Rwork0.213 ---
obs0.213 47173 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.6867 Å2 / ksol: 0.276323 e/Å3
Displacement parametersBiso mean: 52.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å25.13 Å2
2--1.85 Å20 Å2
3----1.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 2.67→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12198 0 60 83 12341
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shellResolution: 2.67→2.84 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.422 364 4.8 %
Rwork0.38 7297 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2PLPconnect2.paramPLPconnect.top
X-RAY DIFFRACTION3water.paramwater.top

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