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- PDB-6ilb: Native crystal structure of fructuronate-tagaturonate epimerase U... -

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Basic information

Entry
Database: PDB / ID: 6ilb
TitleNative crystal structure of fructuronate-tagaturonate epimerase UxaE from Cohnella laeviribosi
ComponentsFructuronate-tagaturonate epimerase UxaE
KeywordsISOMERASE / UxaE / TIM-barrel
Function / homology:
Function and homology information
Biological speciesCohnella laeviribosi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.51 Å
AuthorsChoi, M.Y. / Kang, L.W. / Ho, T.H. / Nguyen, D.Q. / Lee, I.H. / Lee, J.H. / Park, Y.S. / Park, H.J.
CitationJournal: To be published
Title: Crystal structure of fructuronate-tagaturonate epimerase UxaE from Cohnella laeviribosi
Authors: Choi, M.Y. / Kang, L.W. / Ho, T.H. / Nguyen, D.Q. / Lee, I.H. / Lee, J.H. / Park, Y.S. / Park, H.J.
History
DepositionOct 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fructuronate-tagaturonate epimerase UxaE
D: Fructuronate-tagaturonate epimerase UxaE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8426
Polymers110,6082
Non-polymers2344
Water72140
1
A: Fructuronate-tagaturonate epimerase UxaE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4213
Polymers55,3041
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-6 kcal/mol
Surface area20700 Å2
MethodPISA
2
D: Fructuronate-tagaturonate epimerase UxaE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4213
Polymers55,3041
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area360 Å2
ΔGint-3 kcal/mol
Surface area20580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.816, 73.470, 74.673
Angle α, β, γ (deg.)98.140, 110.160, 90.120
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Fructuronate-tagaturonate epimerase UxaE


Mass: 55304.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cohnella laeviribosi (bacteria) / Plasmid: pET29a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: EC: 5.1.2.7
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsWP_019005805.1 for sequence reference

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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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 287 K / Method: evaporation / pH: 8.5
Details: 0.2 M MgCl2, 15% (w/v) PEG 3350, 0.1 M Tris (base)/HCl (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 33313 / % possible obs: 95.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.041 / Rrim(I) all: 0.079 / Χ2: 0.809 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.543.60.40716940.890.2490.4780.53294.7
2.54-2.593.60.36816030.9180.2250.4330.51993
2.59-2.643.60.32616910.9250.20.3840.54195.7
2.64-2.693.50.28716260.9510.1760.3370.54794.2
2.69-2.753.50.25716540.9440.1570.3020.53894
2.75-2.823.50.22516430.9610.140.2660.56794.9
2.82-2.893.50.20516620.9650.1260.2410.5894.5
2.89-2.963.50.17216480.9760.1060.2030.6395.6
2.96-3.053.40.14216520.9830.0880.1680.66294.4
3.05-3.153.20.12116310.9830.080.1460.72595.8
3.15-3.2630.10716720.9840.0750.1320.82194.9
3.26-3.393.20.09516860.9860.0620.1140.94296.4
3.39-3.553.70.08216380.990.0490.0950.99695.5
3.55-3.733.70.07516780.9920.0440.0871.11394.6
3.73-3.973.70.06716680.9930.0390.0771.23796
3.97-4.273.70.05916860.9930.0350.0691.13896.6
4.27-4.73.60.05416740.9950.0330.0631.20295.8
4.7-5.383.50.0516570.9960.0310.0590.97696.1
5.38-6.783.20.04317240.9950.030.0530.80498.8
6.78-503.80.03917260.9970.0230.0460.95698.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.51→48.57 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.909 / SU B: 10.985 / SU ML: 0.246 / SU R Cruickshank DPI: 2.5187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.519 / ESU R Free: 0.334
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2586 1681 5 %RANDOM
Rwork0.1887 ---
obs0.1922 31632 94.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 158.06 Å2 / Biso mean: 61.326 Å2 / Biso min: 33.37 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0.02 Å2-0.01 Å2
2--0.02 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.51→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7784 0 10 40 7834
Biso mean--66.69 54.84 -
Num. residues----978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197950
X-RAY DIFFRACTIONr_bond_other_d0.0020.027312
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.95410728
X-RAY DIFFRACTIONr_angle_other_deg1.018316894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4745976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18323.448406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.404151362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6621566
X-RAY DIFFRACTIONr_chiral_restr0.0870.21154
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028964
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021718
LS refinement shellResolution: 2.505→2.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 94 -
Rwork0.259 2117 -
all-2211 -
obs--84.49 %

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