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- PDB-3ruh: Alternative analogs as viable substrates of UDP-hexose 4-epimerases -

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Basic information

Entry
Database: PDB / ID: 3ruh
TitleAlternative analogs as viable substrates of UDP-hexose 4-epimerases
ComponentsWbgU
KeywordsISOMERASE / Rossmann fold / UDP-hexose 4-epimerase
Function / homology
Function and homology information


UDP-N-acetylglucosamine 4-epimerase / UDP-N-acetylglucosamine 4-epimerase activity / O antigen biosynthetic process / nucleotide binding
Similarity search - Function
UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-UD6 / UDP-N-acetylglucosamine 4-epimerase
Similarity search - Component
Biological speciesPlesiomonas shigelloides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsBhatt, V.S. / Guan, W. / Wang, P.G.
CitationJournal: TO BE PUBLISHED
Title: Alternative analogs as viable substrates of UDP-hexose 4-epimerases
Authors: Bhatt, V.S. / Guan, W. / Wang, P.G.
History
DepositionMay 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: WbgU
B: WbgU
C: WbgU
D: WbgU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,67916
Polymers159,2884
Non-polymers5,39012
Water73941
1
A: WbgU
hetero molecules

D: WbgU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,49510
Polymers79,6442
Non-polymers2,8518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-y,x-y,z-1/31
Buried area4890 Å2
ΔGint-49 kcal/mol
Surface area24740 Å2
MethodPISA
2
B: WbgU
C: WbgU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1846
Polymers79,6442
Non-polymers2,5404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-46 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.612, 76.612, 220.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
WbgU


Mass: 39822.109 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plesiomonas shigelloides (bacteria) / Gene: wbgU / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7BJX9

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Non-polymers , 5 types, 53 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-UD6 / [[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4R,5R,6R)-6-(hydroxymethyl)-4,5-bis(oxidanyl)-3-(2-oxidanylidenepropyl)oxan-2-yl] hydrogen phosphate / UDP-2-ketoGlc


Mass: 606.366 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H28N2O17P2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 300 K / Method: microbatch under oil / pH: 6.5
Details: 25% PEG 3350, 0.2 M Ammonium Sulfate, 200 mM Bis Tris Propane pH 6.5, microbatch under oil, temperature 300K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 6, 2011
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionHighest resolution: 2.88 Å / Num. obs: 30694 / % possible obs: 98.5 %

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LU1

3lu1


Resolution: 2.88→73.53 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.823 / SU B: 42.243 / SU ML: 0.366 / Cross valid method: THROUGHOUT / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26845 1632 5 %RANDOM
Rwork0.20964 ---
obs0.21259 30694 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.037 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å2-0.45 Å2-0 Å2
2---0.91 Å2-0 Å2
3---1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.88→73.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10724 0 348 41 11113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02211324
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1531.98915426
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66151336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58923.969524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.449151844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1751568
X-RAY DIFFRACTIONr_chiral_restr0.0780.21748
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218468
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.241.56668
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.472210788
X-RAY DIFFRACTIONr_scbond_it0.78134656
X-RAY DIFFRACTIONr_scangle_it1.3664.54638
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.88→2.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 105 -
Rwork0.285 2234 -
obs--94.73 %
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)
12.11860.33350.49922.547-0.4111.715-0.0559-0.25590.17280.4190.05570.2821-0.1033-0.19190.00030.1309-0.02880.01860.09230.00740.047724.8461-12.115313.3934
22.00540.26280.7362.5961-0.09521.6494-0.06820.4311-0.1688-0.24730.0368-0.26810.12130.19070.03140.1189-0.04260.01460.1065-0.02430.047315.4021-50.903614.4428
31.63210.3048-0.31482.83430.52792.20590.0505-0.375-0.05640.1741-0.16450.11310.0905-0.02970.11410.0788-0.0125-0.03610.0936-0.00130.067927.9996-42.94251.68
41.6245-0.4290.18862.80850.67461.98790.04180.33480.0671-0.2531-0.15340.0841-0.0468-0.06480.11160.07840.00020.03040.0781-0.00220.0753-10.3092-23.39849.7078
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 341
2X-RAY DIFFRACTION2B1 - 341
3X-RAY DIFFRACTION3C1 - 341
4X-RAY DIFFRACTION4D1 - 341

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