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- PDB-3rua: Specific recognition of N-acetylated substrates and domain flexib... -

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Basic information

Entry
Database: PDB / ID: 3rua
TitleSpecific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase
ComponentsWbgU
KeywordsISOMERASE / UDP-hexose 4-epimerase / domain flexibility / Rossmann fold
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: 2.1 Å
AuthorsBhatt, V.S. / Guan, W. / Wang, P.G.
CitationJournal: TO BE PUBLISHED
Title: Specific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase
Authors: Bhatt, V.S. / Guan, W. / Wang, P.G.
History
DepositionMay 4, 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)162,13414
Polymers159,2884
Non-polymers2,84610
Water6,395355
1
A: WbgU
hetero molecules

D: WbgU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1638
Polymers79,6442
Non-polymers1,5196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_444-y-1,x-y-1,z-1/31
Buried area4660 Å2
ΔGint-40 kcal/mol
Surface area25750 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 area4650 Å2
ΔGint-40 kcal/mol
Surface area25840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.444, 77.444, 224.223
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
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: 103 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
ReflectionResolution: 2.1→50 Å / Num. all: 87898 / Num. obs: 87898 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.1→2.14 Å / % possible all: 100

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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: 2.1→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.85 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23426 4402 5 %RANDOM
Rwork0.17956 ---
obs0.18225 83349 99.84 %-
all-83349 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.667 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.16 Å2-0 Å2
2--0.32 Å2-0 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10724 0 286 355 11365
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02211260
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8831.98115332
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69151336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85523.969524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.397151844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5351568
X-RAY DIFFRACTIONr_chiral_restr0.1440.21728
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218448
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_it0.9351.56668
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.563210788
X-RAY DIFFRACTIONr_scbond_it2.77334592
X-RAY DIFFRACTIONr_scangle_it4.1354.54544
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 326 -
Rwork0.208 6060 -
obs--98.1 %
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)
11.4552-0.33430.63851.8380.12861.2313-0.0433-0.2751-0.06910.22040.030.20720.106-0.18030.01330.07630.01290.02220.0610.00840.035823.2895-28.770712.5989
21.4056-0.35010.41311.8080.50421.1525-0.01020.20070.1583-0.3084-0.0061-0.1665-0.1120.18370.01630.07930.01280.01950.06560.01820.034352.0817-56.726513.8253
31.1259-0.39860.01261.27250.29221.3281-0.0577-0.1369-0.01370.2196-0.01280.00670.01080.05390.07050.06110.0276-0.00290.0843-0.01810.061351.9848-41.580451.7878
41.5539-0.174-0.28390.8339-0.17731.3306-0.05060.2271-0.0096-0.1386-0.02290.018-0.0456-0.03510.07350.05330.02110.01420.09380.01330.059115.2921-65.182449.3963
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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