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- PDB-5tpv: X-ray structure of WlaRA (TDP-fucose-3,4-ketoisomerase) from Camp... -

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Basic information

Entry
Database: PDB / ID: 5tpv
TitleX-ray structure of WlaRA (TDP-fucose-3,4-ketoisomerase) from Campylobacter jejuni
ComponentsWlaRA, TDP-fucose-3,4-ketoisomerase
KeywordsISOMERASE / ketoisomerase / lipooligosaccharide / deoxy-sugar / unusual sugar
Function / homology
Function and homology information


Sugar 3,4-ketoisomerase QdtA, cupin domain / WxcM-like, C-terminal / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / THYMIDINE-5'-DIPHOSPHATE / WxcM-like domain-containing protein
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni 81116 (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsHolden, H.M. / Thoden, J.B. / Li, Z.A. / Riegert, A.S. / Goneau, M.-F. / Cunningham, A.M. / Vinograd, E. / Schoenhofen, I.C. / Gilbert, M. / Li, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115921 United States
CitationJournal: Glycobiology / Year: 2017
Title: Characterization of the dTDP-Fuc3N and dTDP-Qui3N biosynthetic pathways in Campylobacter jejuni 81116.
Authors: Li, Z.Z. / Riegert, A.S. / Goneau, M.F. / Cunningham, A.M. / Vinogradov, E. / Li, J. / Schoenhofen, I.C. / Thoden, J.B. / Holden, H.M. / Gilbert, M.
History
DepositionOct 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 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: WlaRA, TDP-fucose-3,4-ketoisomerase
B: WlaRA, TDP-fucose-3,4-ketoisomerase
C: WlaRA, TDP-fucose-3,4-ketoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5528
Polymers55,1563
Non-polymers1,3975
Water3,801211
1
A: WlaRA, TDP-fucose-3,4-ketoisomerase
B: WlaRA, TDP-fucose-3,4-ketoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7656
Polymers36,7702
Non-polymers9944
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-46 kcal/mol
Surface area12850 Å2
MethodPISA
2
C: WlaRA, TDP-fucose-3,4-ketoisomerase
hetero molecules

C: WlaRA, TDP-fucose-3,4-ketoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5754
Polymers36,7702
Non-polymers8042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area4730 Å2
ΔGint-39 kcal/mol
Surface area12050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.953, 177.953, 88.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-368-

HOH

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Components

#1: Protein WlaRA, TDP-fucose-3,4-ketoisomerase


Mass: 18385.213 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni 81116 (Campylobacter)
Strain: 81116 / Gene: WlaRA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q9ALS3
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 3.18 Å3/Da / Density % sol: 61.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 8-10% PEG-8000, 1.25 M tetraethylammonium chloride, 2% dimethylsulfoxide, 5mM TDP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: LIQUID ANODE / Type: Excillum MetalJet D2+ 160 kV / Wavelength: 1.3418 Å
DetectorDetector: PIXEL / Date: Aug 11, 2016 / Details: BRUKER PHOTON II CPAD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3418 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 39045 / % possible obs: 99.3 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 11.4
Reflection shellResolution: 2.15→2.24 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.8 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TPU

5tpu


Resolution: 2.14→125.83 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.896 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26317 1879 4.8 %RANDOM
Rwork0.20709 ---
obs0.20981 37071 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.419 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å20 Å20 Å2
2---1.62 Å20 Å2
3---3.24 Å2
Refinement stepCycle: 1 / Resolution: 2.14→125.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 85 211 3704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023570
X-RAY DIFFRACTIONr_bond_other_d0.0010.023373
X-RAY DIFFRACTIONr_angle_refined_deg2.1351.9794820
X-RAY DIFFRACTIONr_angle_other_deg0.95437780
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1375401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96125.341176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.28115676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.632157
X-RAY DIFFRACTIONr_chiral_restr0.1340.2517
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023897
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02838
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_it5.114.0811613
X-RAY DIFFRACTIONr_mcbond_other5.1034.0771612
X-RAY DIFFRACTIONr_mcangle_it6.2266.0842011
X-RAY DIFFRACTIONr_mcangle_other6.2256.0892012
X-RAY DIFFRACTIONr_scbond_it7.0554.7661957
X-RAY DIFFRACTIONr_scbond_other6.7664.721941
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.4076.8252785
X-RAY DIFFRACTIONr_long_range_B_refined11.10234.2984142
X-RAY DIFFRACTIONr_long_range_B_other11.12734.1444091
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.141→2.196 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 126 -
Rwork0.294 2560 -
obs--93.56 %

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