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- PDB-3ru7: Specific recognition of N-acetylated substrates and domain flexib... -

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Basic information

Entry
Database: PDB / ID: 3ru7
TitleSpecific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase
ComponentsWbgU
KeywordsISOMERASE / epimerase / Rossmann fold / UDP-GalNAc / 4-epimerase / UDP-hexose 4-epimerase / UDP-hexoses / NAD(H)
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
GLYCINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Unknown ligand / UDP-N-acetylglucosamine 4-epimerase
Similarity search - Component
Biological speciesPlesiomonas shigelloides (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 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. / G Wang, P.
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 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_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)162,37620
Polymers159,2884
Non-polymers3,08816
Water1,72996
1
A: WbgU
C: WbgU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,21111
Polymers79,6442
Non-polymers1,5679
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-61 kcal/mol
Surface area26400 Å2
MethodPISA
2
B: WbgU
hetero molecules

D: WbgU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1659
Polymers79,6442
Non-polymers1,5217
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z+1/31
Buried area4780 Å2
ΔGint-46 kcal/mol
Surface area26270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.730, 77.730, 224.540
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: 39822.105 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 , 6 types, 112 molecules

#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-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#6: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.46 Å3/Da / Density % sol: 49.97 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 6, 2011
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→74.8 Å / Num. all: 46337 / Num. obs: 45596 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0109refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LU1

3lu1


Resolution: 2.6→74.8 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.887 / SU B: 28.765 / SU ML: 0.278 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 2307 5.1 %RANDOM
Rwork0.21686 ---
all0.2196 43276 --
obs0.2196 43276 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.547 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å20 Å2
2--0.5 Å2-0 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.6→74.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10724 0 300 96 11120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211268
X-RAY DIFFRACTIONr_angle_refined_deg1.1681.98215340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.31651336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89323.969524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.295151844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2361568
X-RAY DIFFRACTIONr_chiral_restr0.0810.21728
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218456
X-RAY DIFFRACTIONr_mcbond_it0.3671.56676
X-RAY DIFFRACTIONr_mcangle_it0.698210796
X-RAY DIFFRACTIONr_scbond_it0.96734592
X-RAY DIFFRACTIONr_scangle_it1.6094.54544
LS refinement shellResolution: 2.605→2.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 168 -
Rwork0.288 3247 -
obs--99.16 %
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)
10.9945-0.06540.2051.35840.22251.0988-0.0419-0.1694-0.03470.16110.00940.16570.0357-0.10020.03250.03590.01360.0210.03690.00510.021123.165-28.777613.1317
21.2241-0.09050.32911.18060.12181.0937-0.010.14630.119-0.2081-0.0211-0.11-0.05980.10060.03110.05210.00830.01770.02820.01660.020513.345910.445814.1168
30.6073-0.19160.22041.351-0.16390.9459-0.04010.1244-0.0101-0.1523-0.01490.0220.0116-0.00350.05510.024-0.0124-0.00150.0293-0.00260.011710.0187-21.2184-25.1305
40.65630.1724-0.17121.3944-0.11240.8746-0.0278-0.13850.01260.1446-0.03340.026-0.01410.01840.06120.01920.00720.00280.0303-0.00220.010948.9182-1.1898-22.4734
54.6938-2.3032-5.43161.25791.637514.5547-0.1691-0.3549-0.03050.08250.13330.0140.0880.58490.03570.09380.045-0.05340.047-0.01540.039621.8439-21.913711.0784
614.274-14.77694.551150.42996.8235.2380.0004-0.4573-0.5655-0.0725-0.80013.5029-0.0422-0.57220.79970.20910.0754-0.03510.106-0.12480.30287.573-28.077117.8309
70.3165-0.2141-2.11821.24162.282214.835-0.03850.05470.0075-0.06780.1109-0.0170.0931-0.249-0.07240.13510.041-0.02110.0595-0.01040.0437.978115.018216.1711
839.2003-11.365246.167712.48761.363478.0371-0.9311-0.0992.8580.4302-0.05-2.3086-0.8349-0.2340.9810.17790.0604-0.02370.02380.03130.478420.438124.19199.5116
910.807713.69796.9529.90718.268410.32930.18940.0385-0.30890.4115-0.2281-0.20.2893-0.28030.03870.037-0.0029-0.02510.07510.02060.108515.1315-16.9235-21.9059
1032.29479.99381.62513.13130.51940.089-0.03921.9118-1.47270.13720.2851-0.460.04730.0399-0.24590.3393-0.2280.06150.6313-0.01210.253323.0613-29.3862-30.3531
117.6186-8.5737-5.187117.79956.715417.0227-0.0896-0.38450.0385-0.18370.19120.3841-0.1565-0.0807-0.10160.04120.0150.01940.0880.03050.100853.9935-5.494-25.6933
1274.0546-3.9057-5.12910.20650.27080.3554-0.0242-2.21410.8573-0.010.0998-0.0484-0.00390.1494-0.07560.2660.0046-0.01410.26350.15990.212861.90916.9534-17.2739
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
5X-RAY DIFFRACTION5A349
6X-RAY DIFFRACTION6A350
7X-RAY DIFFRACTION7B349
8X-RAY DIFFRACTION8B350
9X-RAY DIFFRACTION9C349
10X-RAY DIFFRACTION10C350
11X-RAY DIFFRACTION11D349
12X-RAY DIFFRACTION12D350

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