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- PDB-6wj9: UDP-GlcNAc C4-epimerase mutant S121A/Y146F from Pseudomonas prote... -

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Basic information

Entry
Database: PDB / ID: 6wj9
TitleUDP-GlcNAc C4-epimerase mutant S121A/Y146F from Pseudomonas protegens in complex with UDP-GlcNAc
ComponentsNAD-dependent epimerase/dehydratase family protein
KeywordsISOMERASE / Short Chain Dehydrogenase / Complex / NAD dependent
Function / homology
Function and homology information


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 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / NAD-dependent epimerase/dehydratase family protein
Similarity search - Component
Biological speciesPseudomonas protegens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsMarmont, L.S. / Willams, R.J. / Whitney, J.C. / Whitfield, G.B. / Robinson, H. / Parsek, M.R. / Nitz, M. / Harrison, J.J. / Howell, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research Canada
CitationJournal: J.Biol.Chem. / Year: 2020
Title: PelX is a UDP-N-acetylglucosamine C4-epimerase involved in Pel polysaccharide-dependent biofilm formation.
Authors: Marmont, L.S. / Whitfield, G.B. / Pfoh, R. / Williams, R.J. / Randall, T.E. / Ostaszewski, A. / Razvi, E. / Groves, R.A. / Robinson, H. / Nitz, M. / Parsek, M.R. / Lewis, I.A. / Whitney, J.C. ...Authors: Marmont, L.S. / Whitfield, G.B. / Pfoh, R. / Williams, R.J. / Randall, T.E. / Ostaszewski, A. / Razvi, E. / Groves, R.A. / Robinson, H. / Nitz, M. / Parsek, M.R. / Lewis, I.A. / Whitney, J.C. / Harrison, J.J. / Howell, P.L.
History
DepositionApr 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent epimerase/dehydratase family protein
B: NAD-dependent epimerase/dehydratase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8156
Polymers65,2742
Non-polymers2,5424
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-42 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.195, 75.487, 79.271
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Components on special symmetry positions
IDModelComponents
11A-606-

HOH

21A-647-

HOH

31A-686-

HOH

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Components

#1: Protein NAD-dependent epimerase/dehydratase family protein / PelX


Mass: 32636.877 Da / Num. of mol.: 2 / Mutation: C232S, Y146F, S121A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas protegens (bacteria) / Strain: Pf-5 / Gene: PFL_2971 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4KCF6
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 21% PEG 4000, 0.1 M sodium citrate pH 5.6, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.1→50.03 Å / Num. obs: 82655 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 26.33 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 23.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 3685
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SB8

1sb8


Resolution: 2.11→50.03 Å / SU ML: 0.1974 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.4099
RfactorNum. reflection% reflection
Rfree0.1945 3828 4.63 %
Rwork0.1561 --
obs0.1579 82655 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.65 Å2
Refinement stepCycle: LAST / Resolution: 2.11→50.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4529 0 153 450 5132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064773
X-RAY DIFFRACTIONf_angle_d0.86346516
X-RAY DIFFRACTIONf_chiral_restr0.0486758
X-RAY DIFFRACTIONf_plane_restr0.0048842
X-RAY DIFFRACTIONf_dihedral_angle_d14.63062819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.140.25521500.21982638X-RAY DIFFRACTION91.62
2.14-2.160.24381300.19572912X-RAY DIFFRACTION99.8
2.16-2.190.211350.19222956X-RAY DIFFRACTION99.58
2.19-2.220.21821570.17992881X-RAY DIFFRACTION99.54
2.22-2.260.24971380.17532901X-RAY DIFFRACTION99.67
2.26-2.290.22771550.16992962X-RAY DIFFRACTION99.65
2.29-2.330.22991220.17232971X-RAY DIFFRACTION99.84
2.33-2.370.25041480.18092911X-RAY DIFFRACTION99.74
2.37-2.410.2251280.17092888X-RAY DIFFRACTION99.9
2.41-2.460.2141430.16752915X-RAY DIFFRACTION99.77
2.46-2.510.19291450.15832991X-RAY DIFFRACTION99.9
2.51-2.560.18261430.16022883X-RAY DIFFRACTION99.9
2.56-2.620.21261430.16152979X-RAY DIFFRACTION100
2.62-2.690.21341570.15862893X-RAY DIFFRACTION99.9
2.69-2.760.24221390.1712937X-RAY DIFFRACTION99.9
2.76-2.840.2261310.16422954X-RAY DIFFRACTION100
2.84-2.940.22751590.16462906X-RAY DIFFRACTION100
2.94-3.040.19581440.16412933X-RAY DIFFRACTION100
3.04-3.160.19721270.15782943X-RAY DIFFRACTION100
3.16-3.310.1871370.15982971X-RAY DIFFRACTION100
3.31-3.480.20741480.1572891X-RAY DIFFRACTION100
3.48-3.70.19271390.152937X-RAY DIFFRACTION100
3.7-3.980.18121430.1422955X-RAY DIFFRACTION100
3.98-4.380.14841430.13132927X-RAY DIFFRACTION100
4.38-5.020.1541320.11722966X-RAY DIFFRACTION100
5.02-6.320.18051470.15052911X-RAY DIFFRACTION100
6.32-50.030.15321450.15232915X-RAY DIFFRACTION99.64
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)
11.73262469975-0.6049938741420.6511429940731.55663743999-0.1222149523381.37829785341-0.05085248006760.164843893750.2479515727540.0563699911141-0.0550748243792-0.417110953054-0.226889080670.2127328970150.04164907695310.134336452774-0.0617093425007-0.02222056888650.1871307087170.02299928641970.287478817909-8.2315778412821.1451192122-4.86532628552
23.3800128234-0.297615348241-0.7672089597231.44639283099-0.004515577887992.86044067138-0.13399091863-0.3422644427960.2649287331110.3452756384150.0583155444815-0.182688483449-0.2352053215570.03050298049690.03883679622920.2509498021630.0284792543897-0.09863214641070.175761708303-0.0276744451370.244305250108-11.779850018314.149293935213.7207681993
30.8384309098990.4593094874880.4498637685492.68196127501-0.3485566803992.20520661011-0.07759197423790.04728988129230.0988659873049-0.447271369471-0.02070364121990.341809986426-0.526951752621-0.4032407794490.08332658828260.320765946110.105114669322-0.06725691185950.279676631106-0.007110162021490.189342100798-39.67773282630.1608520233-25.678951564
45.14767267593-0.880913301763-0.56363880052.27677779971-0.6470980421893.05157131506-0.05307806485070.2859561703850.0425682008508-0.275287216401-0.151965738826-0.21794417911-0.0279359484730.1938346306860.1976811851830.2264449930990.0019034613694-0.008116486650610.1786708816470.04361295443880.135106410685-25.211967255225.4281166154-18.9160198571
51.010282541980.4828478071091.301350529684.57728967728-0.2708089330752.401560299020.03336369643750.128277320098-0.304149180744-0.0126890362044-0.0584777408321-0.04703017594480.219556708160.02426259680230.02691272225430.1445439620120.01461431425530.002038728504380.2045517942150.006437990276840.120885007565-29.592027877910.1319268805-16.3165775142
60.605691990947-0.0428189061442-0.1055562390842.64164703961.445391032473.38058905074-0.0208312077647-0.0440501697712-0.04609320640780.00950173071566-0.06976836727630.136551904591-0.00261760307438-0.2418337457260.08575880858250.1155477528710.0223230656511-0.01254437779510.1937229098180.01648092646630.140177815803-31.546376399817.8273261946-13.4278090783
70.850973815026-1.08223399924-1.107767516062.042476345332.136287215654.145671507020.06537829139840.05264498439560.00923890703399-0.226491730737-0.02604047031550.0589582974378-0.202135911676-0.134821315609-0.04325361376980.163273291598-0.0457274085476-0.04299621810410.1765562013630.005863617028050.191861494354-33.769876697110.6497986945-32.0234847876
83.33256165925-0.605384624234-0.5274863204515.070898935510.4418463871838.778574727690.01113251447160.0830404541061-0.0449807066416-0.548093488552-0.03589814507650.25057589365-0.163703297980.05771331898530.03547047702370.266631791523-0.063252682091-0.02779696461260.153158111248-0.04183981297130.180322232543-30.36964949492.3129203038-45.9602863546
92.0995999374-1.79205375086-1.688607658441.90628061321.857802953595.154014368940.204611454319-0.5003162016920.02192098357150.1506104100010.177786140055-0.3422972423270.03091809479271.10832479846-0.4192877810760.298819016848-0.0657374307437-0.07239571503690.413554130339-0.04679109833430.285413732908-24.7005999331.95169511344-27.7127061656
102.33819737390.0977379049188-2.002170402340.9829132254840.8630339917487.77649246503-0.01437613917660.0742669230351-0.317712153858-0.136418668829-0.1479173692330.3568313011640.460254775142-1.003735431050.1383357129080.223750518179-0.0211998206821-0.06955922161870.359953789224-0.04516870697980.345294656479-42.86276700677.40035703849-29.7882743744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 177 )
2X-RAY DIFFRACTION2chain 'A' and (resid 178 through 310 )
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 76 )
4X-RAY DIFFRACTION4chain 'B' and (resid 77 through 111 )
5X-RAY DIFFRACTION5chain 'B' and (resid 112 through 144 )
6X-RAY DIFFRACTION6chain 'B' and (resid 145 through 177 )
7X-RAY DIFFRACTION7chain 'B' and (resid 178 through 249 )
8X-RAY DIFFRACTION8chain 'B' and (resid 250 through 270 )
9X-RAY DIFFRACTION9chain 'B' and (resid 271 through 284 )
10X-RAY DIFFRACTION10chain 'B' and (resid 285 through 310 )

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