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- PDB-5tpu: x-ray structure of the WlaRB TDP-quinovose 3,4-ketoisomerase from... -

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Basic information

Entry
Database: PDB / ID: 5tpu
Titlex-ray structure of the WlaRB TDP-quinovose 3,4-ketoisomerase from campylobacter jejuni
ComponentsPutative uncharacterized protein
KeywordsISOMERASE / ketoisomerase / quinovose / deoxy-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
THYMIDINE-5'-DIPHOSPHATE / Sugar 3,4-ketoisomerase QdtA cupin domain-containing protein
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHolden, H.M. / Thoden, J.B. / Li, J.Z. / Riegert, A.S. / Goneau, M.-F. / Cunningham, A.M. / Vinogradov, E. / Schoenhofen, I.C. / Gilbert, M.
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 19, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,92510
Polymers64,2464
Non-polymers1,6806
Water5,170287
1
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9274
Polymers32,1232
Non-polymers8042
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-33 kcal/mol
Surface area12180 Å2
MethodPISA
2
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9986
Polymers32,1232
Non-polymers8754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-56 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.600, 104.600, 93.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Putative uncharacterized protein


Mass: 16061.453 Da / Num. of mol.: 4 / Mutation: E118A, K119A, E120A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Production host: Escherichia coli (E. coli) / Strain (production host): rosetta2(DE3) / References: UniProt: Q9ALS4
#2: Chemical
ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, 16-18% PEG-8000, 200 mM LiCl, 5 mM TDP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jul 16, 2016 / Details: montel
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 39376 / % possible obs: 99.7 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 12.7
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.8 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PA7

2pa7


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.359 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.177 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 2017 5.1 %RANDOM
Rwork0.17946 ---
obs0.18284 37330 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.169 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4300 0 102 287 4689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194498
X-RAY DIFFRACTIONr_bond_other_d0.0020.024312
X-RAY DIFFRACTIONr_angle_refined_deg2.0041.9896072
X-RAY DIFFRACTIONr_angle_other_deg0.95139888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2715526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08323.86228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.22315814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.1071536
X-RAY DIFFRACTIONr_chiral_restr0.1220.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025032
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021084
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_it2.4852.4122104
X-RAY DIFFRACTIONr_mcbond_other2.4742.4112103
X-RAY DIFFRACTIONr_mcangle_it3.4943.6052624
X-RAY DIFFRACTIONr_mcangle_other3.4943.6062625
X-RAY DIFFRACTIONr_scbond_it3.4972.8462394
X-RAY DIFFRACTIONr_scbond_other3.5012.8472386
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3424.0973434
X-RAY DIFFRACTIONr_long_range_B_refined6.94719.9155216
X-RAY DIFFRACTIONr_long_range_B_other6.90119.8185124
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 172 -
Rwork0.28 2701 -
obs--98.93 %

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