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- PDB-5ll2: Structure of Isoleucine 2-epimerase from Lactobacillus buchneri (... -

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Basic information

Entry
Database: PDB / ID: 5ll2
TitleStructure of Isoleucine 2-epimerase from Lactobacillus buchneri (apo 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Isoleucine 2-epimerase
Similarity search - Component
Biological speciesLactobacillus buchneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)211,3874
Polymers211,3874
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17650 Å2
ΔGint-115 kcal/mol
Surface area54230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.160, 161.780, 186.170
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) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M1GRN3, isoleucine 2-epimerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 12 to 18 % PEG3350 and 100 mM Lithium Citrate

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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: 2.6→20 Å / Num. obs: 55147 / % possible obs: 98.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 9.3
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.93 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.806 / SU B: 12.583 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 0.338 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.31599 2752 5 %RANDOM
Rwork0.24387 ---
obs0.24747 52387 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.475 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12549 0 0 26 12575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01912838
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.96117407
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.22951624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90824.846551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.424152142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4331544
X-RAY DIFFRACTIONr_chiral_restr0.1220.21933
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219708
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_it2.9974.3016514
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.7266.4428129
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9344.3926324
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.63836.44819787
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: 2.601→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 202 -
Rwork0.243 3817 -
obs--98.6 %

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