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- PDB-3cqi: Crystal Structure of L-xylulose-5-phosphate 3-epimerase UlaE (for... -

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Basic information

Entry
Database: PDB / ID: 3cqi
TitleCrystal Structure of L-xylulose-5-phosphate 3-epimerase UlaE (form B) complex with sulfate
ComponentsL-ribulose-5-phosphate 3-epimerase ulaE
KeywordsISOMERASE / TIM-barrel / phosphate-binding motif / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


L-ribulose-5-phosphate 3-epimerase / L-ribulose-5-phosphate 3-epimerase activity / intramolecular oxidoreductase activity, interconverting aldoses and ketoses / L-ascorbic acid catabolic process
Similarity search - Function
L-ribulose-5-phosphate 3-epimerase / L-ribulose-5-phosphate 3-epimerase, Enterobacteriaceae / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
L-ribulose-5-phosphate 3-epimerase UlaE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsShi, R. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Bacteriol. / Year: 2008
Title: Structure of L-xylulose-5-Phosphate 3-epimerase (UlaE) from the anaerobic L-ascorbate utilization pathway of Escherichia coli: identification of a novel phosphate binding motif within a TIM barrel fold.
Authors: Shi, R. / Pineda, M. / Ajamian, E. / Cui, Q. / Matte, A. / Cygler, M.
History
DepositionApr 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: L-ribulose-5-phosphate 3-epimerase ulaE
B: L-ribulose-5-phosphate 3-epimerase ulaE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9626
Polymers66,5782
Non-polymers3844
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-59.8 kcal/mol
Surface area21570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.522, 132.529, 82.246
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein L-ribulose-5-phosphate 3-epimerase ulaE / L-xylulose-5- phosphate 3-epimerase / L-ascorbate utilization protein E


Mass: 33288.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 EDL933 / Gene: ulaE / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8XDI5, L-ribulose-5-phosphate 3-epimerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Li2SO4, pH 8.5, vapor diffusion, hanging drop, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9798 Å
DetectorDetector: CCD / Date: Jun 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 31993 / % possible obs: 96.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.069 / Χ2: 0.997 / Net I/σ(I): 11.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1850.40727080.965183.1
2.18-2.266.10.38931070.995195.1
2.26-2.377.10.33131940.991197.6
2.37-2.497.50.24932110.999198.2
2.49-2.657.60.18632110.999198.3
2.65-2.857.60.13632611.002198.6
2.85-3.147.60.09132491198.7
3.14-3.597.60.05432921.001198.9
3.59-4.527.50.03433231.001199.2
4.52-507.10.02834371.001198.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementStarting model: PDB ENTRY 3CQH

3cqh


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.319 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1620 5.1 %RANDOM
Rwork0.185 ---
obs0.187 31975 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.592 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20 Å2
2---1.26 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4376 0 20 186 4582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224498
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.9586086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7055552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85623.846221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44115783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6611538
X-RAY DIFFRACTIONr_chiral_restr0.0830.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023434
X-RAY DIFFRACTIONr_nbd_refined0.1920.22049
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23043
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2244
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.211
X-RAY DIFFRACTIONr_mcbond_it0.6811.52845
X-RAY DIFFRACTIONr_mcangle_it1.08824394
X-RAY DIFFRACTIONr_scbond_it1.6431927
X-RAY DIFFRACTIONr_scangle_it2.5324.51689
LS refinement shellResolution: 2.099→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 101 -
Rwork0.235 1850 -
all-1951 -
obs--81.06 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4712-0.09370.04340.8725-0.21640.416-0.0163-0.05350.02670.1435-0.0043-0.0643-0.04290.0280.0207-0.0050.0165-0.0233-0.0279-0.0061-0.049325.227658.802722.8861
20.41170.22660.08830.7924-0.02360.6737-0.02520.0302-0.0228-0.03310.0187-0.07510.11110.06860.0065-0.01260.03980.029-0.056-0.0128-0.017931.653442.5056-1.0387
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 280
2X-RAY DIFFRACTION1A285
3X-RAY DIFFRACTION1A286
4X-RAY DIFFRACTION1A287
5X-RAY DIFFRACTION2B16 - 28
6X-RAY DIFFRACTION2B31 - 228
7X-RAY DIFFRACTION2B231 - 281
8X-RAY DIFFRACTION2B285

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