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- PDB-3cqh: Crystal Structure of L-xylulose-5-phosphate 3-epimerase UlaE from... -

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Basic information

Entry
Database: PDB / ID: 3cqh
TitleCrystal Structure of L-xylulose-5-phosphate 3-epimerase UlaE from the Anaerobic L-ascorbate Utilization Pathway of Escherichia coli
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 / SAD / Resolution: 2.08 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 / Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software

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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)68,1837
Polymers67,7032
Non-polymers4805
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-87.3 kcal/mol
Surface area20780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.386, 110.386, 103.015
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-468-

HOH

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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: 33851.586 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.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: amonium sulfate, pH 7.0, vapor diffusion, hanging drop, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionRedundancy: 4.9 % / Av σ(I) over netI: 6.7 / Number: 167273 / Rmerge(I) obs: 0.114 / Χ2: 1.02 / D res high: 2.08 Å / D res low: 50 Å / Num. obs: 33828 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.815010010.0461.0045
4.625.8110010.0611.0215
4.034.6210010.0650.9695
3.664.0310010.081.0075
3.43.6610010.1151.0025
3.23.410010.170.9665
3.043.210010.2681.0845
2.913.0410010.3481.1145
2.82.9110010.4541.0565
2.72.810010.511.0354.5
ReflectionResolution: 2.08→50 Å / Num. obs: 38726 / % possible obs: 99.8 % / Redundancy: 7.6 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.074 / Χ2: 0.972 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.08-2.156.10.52738060.8199.9
2.15-2.247.30.42538000.8991100
2.24-2.347.70.32138310.9751100
2.34-2.477.90.20738180.8681100
2.47-2.6280.15738420.8341100
2.62-2.8280.12338351.0111100
2.82-3.1180.08438711.1311100
3.11-3.567.90.06539091.0631100
3.56-4.487.70.05739351.0851100
4.48-507.50.04440790.997198

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se23.8540.3670.7290.0140.616
2Se52.7620.2280.5520.0140.811
3Se47.6570.9620.2520.0050.668
4Se25.9670.1150.7840.0250.646
5Se51.6090.1340.5540.0870.795
6Se32.2360.1320.7380.0820.689
7Se26.6020.3540.780.0690.588
8Se56.2490.7330.1080.0560.851
9Se600.950.2290.0430.91
10Se600.5590.2440.0240.857
11Se26.4230.1440.7150.1270.631
12Se30.8960.3550.9650.0550.591
13Se44.8020.3590.6730.0310.66
14Se35.7370.3470.8060.1120.654
15Se25.5290.1230.840.0310.533
16Se59.9310.7750.3660.0720.613
Phasing dmFOM : 0.69 / FOM acentric: 0.69 / FOM centric: 0.69 / Reflection: 16906 / Reflection acentric: 14623 / Reflection centric: 2283
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.7-49.5410.860.910.78879566313
4.8-7.70.830.860.7324401964476
3.9-4.80.870.880.829922555437
3.4-3.90.780.790.7229242578346
2.9-3.40.60.60.649424450492
2.7-2.90.390.390.3727292510219

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.1phasing
RESOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.08→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / SU B: 9.119 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.208 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1939 5 %RANDOM
Rwork0.212 ---
obs0.214 38665 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.063 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---0.48 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.08→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4033 0 25 169 4227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224138
X-RAY DIFFRACTIONr_angle_refined_deg1.2761.9615593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0655506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65223.744203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43915720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4331538
X-RAY DIFFRACTIONr_chiral_restr0.0980.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023140
X-RAY DIFFRACTIONr_nbd_refined0.2090.21972
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22775
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4390.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.214
X-RAY DIFFRACTIONr_mcbond_it0.9611.52622
X-RAY DIFFRACTIONr_mcangle_it1.38124050
X-RAY DIFFRACTIONr_scbond_it1.97831752
X-RAY DIFFRACTIONr_scangle_it3.0614.51541
LS refinement shellResolution: 2.081→2.135 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 138 -
Rwork0.282 2656 -
all-2794 -
obs--99.93 %
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)
10.98880.28480.32260.90290.07730.270.08050.0283-0.1029-0.0581-0.0522-0.08260.06620.0384-0.0283-0.04740.00420.0046-0.01140.0058-0.007735.943615.322229.5564
20.97210.0835-0.08940.782-0.07830.1980.096700.2005-0.0464-0.03620.1017-0.0404-0.0212-0.0605-0.06760.00780.0265-0.0226-0.01280.031217.779938.093927.6708
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 28116 - 292
2X-RAY DIFFRACTION2BB6 - 28017 - 291

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