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- PDB-6vo6: Crystal Structure of Cj1427, an Essential NAD-dependent Dehydroge... -

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Basic information

Entry
Database: PDB / ID: 6vo6
TitleCrystal Structure of Cj1427, an Essential NAD-dependent Dehydrogenase from Campylobacter jejuni, in the Presence of NADH and GDP
ComponentsPutative sugar-nucleotide epimerase/dehydratease
KeywordsOXIDOREDUCTASE / capsular polysaccharide / isomerase
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With other, known, physiological acceptors / UDP-glucose 4-epimerase activity / capsule polysaccharide biosynthetic process / NADH binding / GDP binding / protein homotetramerization / oxidoreductase activity / identical protein binding
Similarity search - Function
: / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / TETRAMETHYLAMMONIUM ION / GDP-D-glycero-alpha-D-manno-heptose dehydrogenase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsAnderson, T.K. / Spencer, K.D. / Thoden, J.B. / Huddleston, J.P. / Raushel, F.M. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122825 United States
CitationJournal: Biochemistry / Year: 2020
Title: Structural Analysis of Cj1427, an Essential NAD-Dependent Dehydrogenase for the Biosynthesis of the Heptose Residues in the Capsular Polysaccharides ofCampylobacter jejuni.
Authors: Huddleston, J.P. / Anderson, T.K. / Spencer, K.D. / Thoden, J.B. / Raushel, F.M. / Holden, H.M.
History
DepositionJan 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Putative sugar-nucleotide epimerase/dehydratease
B: Putative sugar-nucleotide epimerase/dehydratease
C: Putative sugar-nucleotide epimerase/dehydratease
D: Putative sugar-nucleotide epimerase/dehydratease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,66130
Polymers146,8774
Non-polymers4,78426
Water23,3651297
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23450 Å2
ΔGint-72 kcal/mol
Surface area43810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.608, 84.343, 135.450
Angle α, β, γ (deg.)90.000, 96.970, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative sugar-nucleotide epimerase/dehydratease


Mass: 36719.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168) (Campylobacter)
Strain: ATCC 700819 / NCTC 11168 / Gene: Cj1427c / Production host: Escherichia coli (E. coli) / Strain (production host): Roesetta2(DE3) / References: UniProt: Q0P8I7, UDP-glucose 4-epimerase

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Non-polymers , 7 types, 1323 molecules

#2: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-TMA / TETRAMETHYLAMMONIUM ION


Mass: 74.145 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H12N
#7: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1297 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 8-11% PEG-8000, 1 M tetramethylammonium chloride, 100 mM homopipes; in the presence of 5 mM GDP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 229896 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.079 / Net I/σ(I): 32.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 11032 / Rsym value: 0.302 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
CRANKphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→35.14 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.216 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.067
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1887 11613 5.1 %RANDOM
Rwork0.1626 ---
obs0.1639 218283 97.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.33 Å2 / Biso mean: 19.406 Å2 / Biso min: 8.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20.28 Å2
2---0.15 Å20 Å2
3----0.87 Å2
Refinement stepCycle: final / Resolution: 1.5→35.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9781 0 311 1297 11389
Biso mean--19.97 31.83 -
Num. residues----1225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01310424
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179817
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.65814103
X-RAY DIFFRACTIONr_angle_other_deg1.4891.58322792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05751256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09722.472538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.867151858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4681563
X-RAY DIFFRACTIONr_chiral_restr0.0990.21376
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211422
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022175
LS refinement shellResolution: 1.501→1.54 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 805 -
Rwork0.231 15384 -
all-16189 -
obs--92.74 %

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