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

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Basic information

Entry
Database: PDB / ID: 3rud
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 activity / UDP-N-acetylglucosamine 4-epimerase / 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 / Unknown ligand / UDP-N-acetylglucosamine 4-epimerase
Similarity search - Component
Biological speciesPlesiomonas shigelloides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Sep 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)161,94212
Polymers159,2884
Non-polymers2,6548
Water4,972276
1
A: WbgU
hetero molecules

D: WbgU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9716
Polymers79,6442
Non-polymers1,3274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z+1/31
Buried area4540 Å2
ΔGint-30 kcal/mol
Surface area26210 Å2
MethodPISA
2
B: WbgU
C: WbgU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9716
Polymers79,6442
Non-polymers1,3274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-30 kcal/mol
Surface area26160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.185, 78.185, 224.818
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#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
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 298.15 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 298.15K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / 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
ReflectionResolution: 2.3→75.9 Å / Num. all: 64466 / Num. obs: 64466 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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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: 2.3→74.94 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.932 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25153 3443 5.1 %RANDOM
Rwork0.1987 ---
all0.20136 64466 --
obs0.20136 64466 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.231 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.09 Å2-0 Å2
2---0.18 Å2-0 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.3→74.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10724 0 276 276 11276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02211251
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.97715317
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44251336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93623.969524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.721151844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0051568
X-RAY DIFFRACTIONr_chiral_restr0.1190.21712
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218448
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_it0.9161.56668
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.645210788
X-RAY DIFFRACTIONr_scbond_it2.65234583
X-RAY DIFFRACTIONr_scangle_it4.074.54529
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.302→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 252 -
Rwork0.224 4764 -
obs--99.72 %

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