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- PDB-6wn6: Crystal structure of 3-keto-D-glucoside 4-epimerase, YcjR, from E... -

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Basic information

Entry
Database: PDB / ID: 6wn6
TitleCrystal structure of 3-keto-D-glucoside 4-epimerase, YcjR, from E. coli, apo form
Components3-keto-D-glucoside 4-epimerase
KeywordsISOMERASE / microbiome / prebiotic / epimerase
Function / homology
Function and homology information


Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives / racemase and epimerase activity, acting on carbohydrates and derivatives / manganese ion binding / carbohydrate metabolic process / cytosol
Similarity search - Function
Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
: / Transient receptor potential locus / 3-dehydro-D-guloside 4-epimerase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsMabanglo, M.F. / Raushel, F.M. / Mukherjee, K.
Funding support United States, 1items
OrganizationGrant numberCountry
Robert A. Welch FoundationA-840 United States
CitationJournal: Biochemistry / Year: 2020
Title: Structure and Reaction Mechanism of YcjR, an Epimerase That Facilitates the Interconversion of d-Gulosides to d-Glucosides inEscherichia coli.
Authors: Mabanglo, M.F. / Huddleston, J.P. / Mukherjee, K. / Taylor, Z.W. / Raushel, F.M.
History
DepositionApr 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 6, 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

Downloads & links

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Assembly

Deposited unit
A: 3-keto-D-glucoside 4-epimerase
B: 3-keto-D-glucoside 4-epimerase
C: 3-keto-D-glucoside 4-epimerase
D: 3-keto-D-glucoside 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,47772
Polymers142,2844
Non-polymers4,19268
Water7,548419
1
A: 3-keto-D-glucoside 4-epimerase
B: 3-keto-D-glucoside 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,11434
Polymers71,1422
Non-polymers1,97232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 3-keto-D-glucoside 4-epimerase
D: 3-keto-D-glucoside 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,36238
Polymers71,1422
Non-polymers2,22036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.576, 116.576, 247.725
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
3-keto-D-glucoside 4-epimerase / Transient receptor potential locus


Mass: 35571.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ycjR, PGD_01932 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5E8GIH3, UniProt: P76044*PLUS
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M sodium malonate, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979231 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979231 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 143197 / % possible obs: 100 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.027 / Rrim(I) all: 0.104 / Χ2: 1.464 / Net I/σ(I): 8.3 / Num. measured all: 2113171
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.86-1.8914.90.93970690.9130.250.9721.015100
1.89-1.9314.90.8170230.9240.2150.8381.012100
1.93-1.9614.90.6670860.9530.1750.6841.024100
1.96-214.90.54570640.9690.1450.5641.05100
2-2.0514.90.45270770.9740.120.4681.06100
2.05-2.0914.90.38770580.980.1030.4011.076100
2.09-2.1514.90.32170730.9850.0850.3321.089100
2.15-2.2114.90.27171310.9910.0720.281.108100
2.21-2.2714.90.22670680.9930.060.2341.162100
2.27-2.3414.90.20271140.9940.0540.2091.175100
2.34-2.4314.90.18771460.9950.050.1931.242100
2.43-2.5214.90.16270890.9950.0430.1671.371100
2.52-2.6414.90.1471440.9960.0380.1451.4100
2.64-2.7814.90.11771540.9970.0310.1211.408100
2.78-2.9514.80.09171470.9980.0240.0941.47100
2.95-3.1814.70.07872250.9990.0210.0811.674100
3.18-3.514.70.06672080.9990.0180.0692.155100
3.5-4.0114.60.04972790.9990.0130.0512.041100
4.01-5.0514.30.042734010.0110.0442.249100
5.05-5013.40.05177020.9990.0140.0533.56599.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→35.91 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.37
RfactorNum. reflection% reflection
Rfree0.1985 1978 1.4 %
Rwork0.1755 --
obs0.1758 141124 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.92 Å2 / Biso mean: 24.847 Å2 / Biso min: 11.14 Å2
Refinement stepCycle: final / Resolution: 1.86→35.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8471 0 260 419 9150
Biso mean--30.57 30.24 -
Num. residues----1055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078698
X-RAY DIFFRACTIONf_angle_d0.79511766
X-RAY DIFFRACTIONf_dihedral_angle_d19.5453262
X-RAY DIFFRACTIONf_chiral_restr0.0541254
X-RAY DIFFRACTIONf_plane_restr0.0041563
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.86-1.910.25361310.21589480961195
1.91-1.960.19641400.1969551969196
1.96-2.020.19731390.18029677981697
2.02-2.080.20181390.1679791993098
2.08-2.160.22811400.179813995398
2.16-2.240.19361400.164598681000899
2.24-2.340.1741400.167398911003199
2.34-2.470.20691400.169599211006199
2.47-2.620.17861420.1663997410116100
2.62-2.820.18281430.16721004310186100
2.82-3.110.18861440.16941009110235100
3.11-3.560.18021430.17771014910292100
3.56-4.480.211450.17921026210407100
4.48-35.910.21041520.18021063510787100
Refinement TLS params.Method: refined / Origin x: 67.2187 Å / Origin y: 115.9372 Å / Origin z: 38.2786 Å
111213212223313233
T0.1424 Å20.0063 Å2-0.0037 Å2-0.1232 Å2-0.0032 Å2--0.1533 Å2
L0.1766 °2-0.0291 °2-0.0436 °2-0.2431 °20.0758 °2--0.5363 °2
S-0.025 Å °0.0072 Å °-0.0116 Å °0.0066 Å °-0.0205 Å °0.0249 Å °-0.0089 Å °-0.0404 Å °0.0376 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 265
2X-RAY DIFFRACTION1allB2 - 265
3X-RAY DIFFRACTION1allC2 - 265
4X-RAY DIFFRACTION1allD2 - 265
5X-RAY DIFFRACTION1allG1 - 4
6X-RAY DIFFRACTION1allS1 - 965
7X-RAY DIFFRACTION1allE1 - 88

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