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- PDB-8v4h: X-ray structure of the NADP-dependent reductase from Campylobacte... -

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Basic information

Entry
Database: PDB / ID: 8v4h
TitleX-ray structure of the NADP-dependent reductase from Campylobacter jejuni responsible for the synthesis of CDP-glucitol in the presence of CDP-glucitol
ComponentsPutative nucleotide sugar dehydratase
KeywordsOXIDOREDUCTASE / capsular polysaccharide / short chain dehydrogenase
Function / homologyOxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / oxidoreductase activity / NAD(P)-binding domain superfamily / nucleotide binding / PHOSPHATE ION / Chem-YCX / CDP-6-D-glucitol synthase
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsThoden, J.B. / Schumann, M.E. / Holden, H.M. / Raushel, F.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134643 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 139428 United States
CitationJournal: Biochemistry / Year: 2024
Title: Biosynthesis of Cytidine Diphosphate-6-d-Glucitol for the Capsular Polysaccharides of Campylobacter jejuni.
Authors: Ghosh, M.K. / Narindoshvili, T. / Thoden, J.B. / Schumann, M.E. / Holden, H.M. / Raushel, F.M.
History
DepositionNov 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative nucleotide sugar dehydratase
B: Putative nucleotide sugar dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5128
Polymers82,1892
Non-polymers1,3246
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-68 kcal/mol
Surface area26870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.760, 101.593, 133.304
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative nucleotide sugar dehydratase


Mass: 41094.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: HS:5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: A0A0U3AP28

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Non-polymers , 5 types, 199 molecules

#2: Chemical ChemComp-YCX / [[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-2,3,4,5,6-pentakis(oxidanyl)hexyl] hydrogen phosphate


Mass: 567.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H27N3O16P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein incubated with 5 mM CDP-glucitol and 5 mN NADPH. Precipitant: 10-14 % w/v poly(ethylene glycol) 8000, 200 mM LiCl, and 100 mM HEPPS (pH 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54178 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jun 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 37429 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Rsym value: 0.073 / Net I/σ(I): 16.4
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4430 / Rsym value: 0.38 / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.06 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.869 / SU B: 8.926 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.319 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28217 1897 5.1 %RANDOM
Rwork0.20672 ---
obs0.21056 35532 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.918 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.03 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.2→39.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5484 0 80 193 5757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125678
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165575
X-RAY DIFFRACTIONr_angle_refined_deg1.581.6587673
X-RAY DIFFRACTIONr_angle_other_deg0.4951.58312854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1695682
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.656522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.527101094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2894
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021265
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_it3.0233.3062710
X-RAY DIFFRACTIONr_mcbond_other3.023.3072710
X-RAY DIFFRACTIONr_mcangle_it4.7815.9313386
X-RAY DIFFRACTIONr_mcangle_other4.785.9323387
X-RAY DIFFRACTIONr_scbond_it3.1883.5982968
X-RAY DIFFRACTIONr_scbond_other3.1893.5982963
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2456.4474275
X-RAY DIFFRACTIONr_long_range_B_refined7.69531.226604
X-RAY DIFFRACTIONr_long_range_B_other7.69231.216568
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 132 -
Rwork0.311 2485 -
obs--93.03 %

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