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- PDB-6vo8: X-ray structure of the Cj1427 in the presence of NADH and GDP-D-g... -

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Basic information

Entry
Database: PDB / ID: 6vo8
TitleX-ray structure of the Cj1427 in the presence of NADH and GDP-D-glycero-D-mannoheptose, an essential NAD-dependent dehydrogenase from Campylobacter jejuni
ComponentsPutative sugar-nucleotide epimerase/dehydratease
KeywordsOXIDOREDUCTASE / capsular polysaccharide / dehydrogenase / 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
Chem-GZ0 / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / GDP-D-glycero-alpha-D-manno-heptose dehydrogenase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSpencer, K.D. / Anderson, T.K. / 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 1.0Mar 25, 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 1.2Oct 11, 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: Putative sugar-nucleotide epimerase/dehydratease
B: Putative sugar-nucleotide epimerase/dehydratease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0406
Polymers73,4392
Non-polymers2,6024
Water3,495194
1
A: Putative sugar-nucleotide epimerase/dehydratease
B: Putative sugar-nucleotide epimerase/dehydratease
hetero molecules

A: Putative sugar-nucleotide epimerase/dehydratease
B: Putative sugar-nucleotide epimerase/dehydratease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,08012
Polymers146,8774
Non-polymers5,2038
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)98.723, 98.852, 72.939
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Putative sugar-nucleotide epimerase/dehydratease


Mass: 36719.281 Da / Num. of mol.: 2
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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: Q0P8I7, UDP-glucose 4-epimerase
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GZ0 / [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S},5~{S},6~{S})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate


Mass: 635.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N5O17P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 8-10% PEG-8000, 2%-tertbutyl alcohol, 100 mM homopipes, in the presence of 2.5 mM GDP-D-glycero-D-mannoheptose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Dec 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 28260 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Rsym value: 0.096 / Net I/σ(I): 13.3
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3 / Num. unique obs: 3174 / Rsym value: 0.351 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6vo6

6vo6


Resolution: 2.4→30.01 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.83 / SU B: 11.675 / SU ML: 0.258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.469 / ESU R Free: 0.309
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2856 1590 5.6 %RANDOM
Rwork0.2063 ---
obs0.2107 26677 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 89.06 Å2 / Biso mean: 25.831 Å2 / Biso min: 1.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.4→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4801 0 170 194 5165
Biso mean--19.68 19.13 -
Num. residues----602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135082
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174724
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.6986888
X-RAY DIFFRACTIONr_angle_other_deg1.2321.60510979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4935599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2822.619252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.8215893
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0611528
X-RAY DIFFRACTIONr_chiral_restr0.0770.2678
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025497
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021059
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 118 -
Rwork0.337 1893 -
all-2011 -
obs--96.92 %

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