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- PDB-5ll3: Structure of the Isoleucine 2-epimerase from Lactobacillus buchne... -

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Basic information

Entry
Database: PDB / ID: 5ll3
TitleStructure of the Isoleucine 2-epimerase from Lactobacillus buchneri (PLP complex form)
ComponentsIsoleucine 2-epimerase
KeywordsISOMERASE / racemase / epimerase / Isoleucine / PLP / Lactobacillus buchneri
Function / homology
Function and homology information


isoleucine 2-epimerase / transaminase activity / isomerase activity / pyridoxal phosphate binding / identical protein binding
Similarity search - Function
: / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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 ...: / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Isoleucine 2-epimerase
Similarity search - Component
Biological speciesLactobacillus buchneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsReiser, J.-B. / Awad, R. / Gans, P.
CitationJournal: Biochimie / Year: 2017
Title: Structural insights into the substrate recognition and reaction specificity of the PLP-dependent fold-type I isoleucine 2-epimerase from Lactobacillus buchneri.
Authors: Awad, R. / Gans, P. / Reiser, J.B.
History
DepositionJul 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Aug 16, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoleucine 2-epimerase
B: Isoleucine 2-epimerase
C: Isoleucine 2-epimerase
D: Isoleucine 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,3768
Polymers211,3874
Non-polymers9894
Water14,052780
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21470 Å2
ΔGint-121 kcal/mol
Surface area52160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.460, 165.400, 188.320
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
Isoleucine 2-epimerase / BCAA racemase


Mass: 52846.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus buchneri (bacteria) / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M1GRN3, isoleucine 2-epimerase
#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.: 780 / 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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12 to 18 % PEG3350 and 100 mM Lithium Citrate, soaking in 1.3 mM PLP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 98052 / % possible obs: 99.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 14.5
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 7 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 3.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EO5

2eo5


Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.932 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.183 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 4953 5.1 %RANDOM
Rwork0.17657 ---
obs0.17865 93099 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.966 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12856 0 60 780 13696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01913228
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.471.96317951
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17851666
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81824.789568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.842152173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.481544
X-RAY DIFFRACTIONr_chiral_restr0.1110.21981
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110020
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_it1.3872.936670
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2954.3868331
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9863.2026558
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.7725.33321032
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: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 363 -
Rwork0.267 6785 -
obs--99.76 %

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