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- PDB-2ykx: Structural Determinants of the Beta-Selectivity of a Bacterial Am... -

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Basic information

Entry
Database: PDB / ID: 2ykx
TitleStructural Determinants of the Beta-Selectivity of a Bacterial Aminotransferase
ComponentsBETA-TRANSAMINASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding
Similarity search - Function
Aminotransferase class-III / Aminotransferase class-III / 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-III / Aminotransferase class-III / 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
2-OXOGLUTARIC ACID / PYRIDOXAL-5'-PHOSPHATE / Beta-transaminase
Similarity search - Component
Biological speciesMESORHIZOBIUM SP. LUK (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWybenga, G.G. / Crismaru, C.G. / Janssen, D.B. / Dijkstra, B.W.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Determinants of the Beta-Selectivity of a Bacterial Aminotransferase.
Authors: Wybenga, G.G. / Crismaru, C.G. / Janssen, D.B. / Dijkstra, B.W.
History
DepositionMay 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Other
Revision 1.2Aug 29, 2012Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _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: BETA-TRANSAMINASE
B: BETA-TRANSAMINASE
C: BETA-TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,39115
Polymers148,7783
Non-polymers1,61212
Water16,898938
1
A: BETA-TRANSAMINASE
B: BETA-TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,2189
Polymers99,1862
Non-polymers1,0337
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-43.4 kcal/mol
Surface area27220 Å2
MethodPISA
2
C: BETA-TRANSAMINASE
hetero molecules

C: BETA-TRANSAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,34412
Polymers99,1862
Non-polymers1,15910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11220 Å2
ΔGint-32.5 kcal/mol
Surface area26740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.761, 94.422, 103.729
Angle α, β, γ (deg.)90.00, 113.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein BETA-TRANSAMINASE / BETA-PHENYLALANINE AMINOTRANSFERASE


Mass: 49592.793 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MESORHIZOBIUM SP. LUK (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A3EYF7

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Non-polymers , 5 types, 950 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 938 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsPLP: SCHIFF BASE BETWEEN K280 ETA-AMINE AND THE C4A OF THE PLP COFACTOR

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.6 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorDate: Apr 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.85→48.23 Å / Num. obs: 138206 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.1
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MES_BFAT_HOLO

Resolution: 1.85→48.23 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.294 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1965 6862 5 %RANDOM
Rwork0.17614 ---
obs0.17715 131343 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.309 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20.64 Å2
2---0.13 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.85→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9668 0 103 938 10709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02110119
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9551.95513711
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.14151331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30922.431469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.265151522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.77115102
X-RAY DIFFRACTIONr_chiral_restr0.0670.21493
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217946
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.2771.56460
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.553210210
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.91533659
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6264.53494
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 484 -
Rwork0.24 9664 -
obs--100 %

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