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- PDB-3ru9: Specific recognition of N-acetylated substrates and domain flexib... -

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Basic information

Entry
Database: PDB / ID: 3ru9
TitleSpecific recognition of N-acetylated substrates and domain flexibility in WbgU: a UDP-GalNAc 4-epimerase
ComponentsWbgU
KeywordsISOMERASE / NAD(H) / UDP-hexose 4-epimerase / domain flexibility
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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 1.2Jan 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)162,28416
Polymers159,2884
Non-polymers2,99612
Water5,639313
1
A: WbgU
C: WbgU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2389
Polymers79,6442
Non-polymers1,5947
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-41 kcal/mol
Surface area26220 Å2
MethodPISA
2
B: WbgU
hetero molecules

D: WbgU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0467
Polymers79,6442
Non-polymers1,4025
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_664-y+1,x-y+1,z-1/31
Buried area4700 Å2
ΔGint-40 kcal/mol
Surface area26230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.410, 77.410, 224.887
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, 325 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 4 / Source method: obtained synthetically
#5: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 49.64 %
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 298.15 K

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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(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→38.8 Å / Num. all: 75624 / Num. obs: 75624 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.2→2.33 Å / % possible all: 100

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Processing

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

3lu1


Resolution: 2.21→38.8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 12.746 / SU ML: 0.146 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23194 3800 5 %RANDOM
Rwork0.1809 ---
all0.18348 71620 --
obs0.18348 71620 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.412 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.21→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10724 0 296 313 11333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02211268
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.98215340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69751336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.11223.969524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.744151844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5161568
X-RAY DIFFRACTIONr_chiral_restr0.1280.21728
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218456
X-RAY DIFFRACTIONr_mcbond_it0.891.56676
X-RAY DIFFRACTIONr_mcangle_it1.564210796
X-RAY DIFFRACTIONr_scbond_it2.7834592
X-RAY DIFFRACTIONr_scangle_it4.2974.54544
LS refinement shellResolution: 2.21→2.267 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 284 -
Rwork0.238 5320 -
obs--99.41 %
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)
11.9350.29480.79552.2655-0.13111.5017-0.01230.372-0.088-0.25670.0039-0.29310.1190.24490.00830.0750.00350.02130.0806-0.00690.043415.5155-6.5849-13.6691
21.8410.31930.53252.2421-0.56381.5206-0.0392-0.27820.20640.34630.02360.2271-0.1492-0.22610.01570.07380.00170.01880.082-0.01690.043625.225132.5025-14.8777
31.00690.27280.22261.81140.20271.51250.0171-0.21520.02820.1507-0.10250.06240.0734-0.00880.08530.0692-0.0136-0.00760.0541-0.01680.052728.25451.217224.4235
41.0037-0.3305-0.25811.92230.24121.51690.01630.225-0.0082-0.169-0.10190.0463-0.0811-0.02370.08560.06650.01090.00140.0569-0.0130.0507-10.438221.152421.989
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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