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- PDB-4lql: Crystal structure of L-arabinose isomerase from Lactobacillus fer... -

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Basic information

Entry
Database: PDB / ID: 4lql
TitleCrystal structure of L-arabinose isomerase from Lactobacillus fermentum CGMCC2921
ComponentsL-arabinose isomerase
KeywordsISOMERASE / hexamer / isomerization
Function / homology
Function and homology information


L-arabinose isomerase / L-arabinose isomerase activity / L-arabinose catabolic process to D-xylulose 5-phosphate / metal ion binding / cytosol
Similarity search - Function
Rossmann fold - #10940 / L-arabinose isomerase / L-arabinose isomerase, C-terminal / L-arabinose isomerase, N-terminal domain superfamily / L-arabinose isomerase N-terminal domain / L-arabinose isomerase C-terminal domain / L-fucose/L-arabinose isomerase, C-terminal / L-fucose isomerase, N-terminal/central domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-arabinose isomerase
Similarity search - Component
Biological speciesLactobacillus fermentum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.232 Å
AuthorsXu, Z.
CitationJournal: to be published
Title: Crystal structure of L-arabinose isomerase from Lactobacillus fermentum CGMCC2921
Authors: Xu, Z.
History
DepositionJul 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: L-arabinose isomerase
B: L-arabinose isomerase
C: L-arabinose isomerase
D: L-arabinose isomerase
E: L-arabinose isomerase
F: L-arabinose isomerase


Theoretical massNumber of molelcules
Total (without water)320,9536
Polymers320,9536
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27220 Å2
ΔGint-208 kcal/mol
Surface area101720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.201, 184.831, 186.347
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
L-arabinose isomerase / LFAI


Mass: 53492.164 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Lactobacillus fermentum (bacteria) / References: UniProt: D9ILD9, L-arabinose isomerase

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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: 2.29 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M Bis-Tris, 25% PEGMME5000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.054 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.054 Å / Relative weight: 1
ReflectionResolution: 3.23→46.59 Å / Num. all: 90230 / Num. obs: 47550 / % possible obs: 99 % / Biso Wilson estimate: 94.79 Å2 / Rmerge(I) obs: 0.102
Reflection shellHighest resolution: 3.23 Å / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AJT

2ajt


Resolution: 3.232→44.849 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.5237 / SU ML: 0.85 / σ(F): 1.35 / Phase error: 50.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4316 2404 5.06 %
Rwork0.3143 --
obs0.3203 47536 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 265.02 Å2 / Biso mean: 80.7835 Å2 / Biso min: 13.76 Å2
Refinement stepCycle: LAST / Resolution: 3.232→44.849 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18516 0 0 0 18516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01118784
X-RAY DIFFRACTIONf_angle_d1.62225428
X-RAY DIFFRACTIONf_chiral_restr0.1012956
X-RAY DIFFRACTIONf_plane_restr0.0063298
X-RAY DIFFRACTIONf_dihedral_angle_d16.2525878
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2316-3.29750.48381330.36462255238886
3.2975-3.36920.47121460.352526322778100
3.3692-3.44750.44981500.323226392789100
3.4475-3.53370.43641350.311926292764100
3.5337-3.62920.45241360.308926672803100
3.6292-3.73590.4471480.295526272775100
3.7359-3.85650.43891450.295226612806100
3.8565-3.99420.42781230.308126522775100
3.9942-4.1540.50991400.330626622802100
4.154-4.34290.47041430.32726642807100
4.3429-4.57170.40161320.294526782810100
4.5717-4.85780.43631470.291426652812100
4.8578-5.23240.42321360.306326912827100
5.2324-5.7580.49321350.354927032838100
5.758-6.58890.49391450.353227312876100
6.5889-8.29270.39891490.3227302879100
8.2927-44.85380.37151610.29082846300799

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