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- PDB-6ds1: Crystal structure of Cj0485 dehydrogenase in complex with NADP+ -

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Basic information

Entry
Database: PDB / ID: 6ds1
TitleCrystal structure of Cj0485 dehydrogenase in complex with NADP+
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / dehydrogenase
Function / homologyEnoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Putative oxidoreductase
Function and homology information
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.119 Å
AuthorsPluvinage, B. / Boraston, A.B.
CitationJournal: Commun Biol / Year: 2020
Title: The gastrointestinal pathogen Campylobacter jejuni metabolizes sugars with potential help from commensal Bacteroides vulgatus.
Authors: Garber, J.M. / Nothaft, H. / Pluvinage, B. / Stahl, M. / Bian, X. / Porfirio, S. / Enriquez, A. / Butcher, J. / Huang, H. / Glushka, J. / Line, E. / Gerlt, J.A. / Azadi, P. / Stintzi, A. / ...Authors: Garber, J.M. / Nothaft, H. / Pluvinage, B. / Stahl, M. / Bian, X. / Porfirio, S. / Enriquez, A. / Butcher, J. / Huang, H. / Glushka, J. / Line, E. / Gerlt, J.A. / Azadi, P. / Stintzi, A. / Boraston, A.B. / Szymanski, C.M.
History
DepositionJun 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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 oxidoreductase
B: Putative oxidoreductase
C: Putative oxidoreductase
D: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,43415
Polymers122,0874
Non-polymers3,34711
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21690 Å2
ΔGint-121 kcal/mol
Surface area33720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.504, 68.462, 70.718
Angle α, β, γ (deg.)89.310, 113.430, 115.670
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative oxidoreductase /


Mass: 30521.822 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: Cj0485 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0PB28
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 23-26% PEG 4000, 0.08 M Tris, 0.15 M MgCl2 (H2O)6 and 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.119→30 Å / Num. obs: 57901 / % possible obs: 95.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 25.69 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.059 / Net I/σ(I): 11.3
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.77 / Rpim(I) all: 0.299 / % possible all: 95.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DRR

6drr


Resolution: 2.119→29.464 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 22.85
RfactorNum. reflection% reflection
Rfree0.2139 2805 4.98 %
Rwork0.1588 --
obs0.1617 56342 95.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.74 Å2 / Biso mean: 27.3872 Å2 / Biso min: 10.04 Å2
Refinement stepCycle: final / Resolution: 2.119→29.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8068 0 214 471 8753
Biso mean--28.04 30.88 -
Num. residues----1037
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1189-2.15550.2401560.1721454151051
2.1555-2.19460.26721020.19142265236779
2.1946-2.23680.30731020.18712411251386
2.2368-2.28250.28491290.18682656278593
2.2825-2.33210.2561600.18172655281597
2.3321-2.38630.2621580.16972789294799
2.3863-2.4460.25641520.169128503002100
2.446-2.51210.26861420.170927782920100
2.5121-2.58590.25911270.163528222949100
2.5859-2.66940.25471460.170427862932100
2.6694-2.76470.24451570.180428202977100
2.7647-2.87530.26691290.169828422971100
2.8753-3.0060.23781240.168228412965100
3.006-3.16440.22331460.169228172963100
3.1644-3.36230.19671480.157827972945100
3.3623-3.62150.21710.147828132984100
3.6215-3.98520.20421720.144427642936100
3.9852-4.560.17281730.138227972970100
4.56-5.73820.17931520.142627952947100
5.7382-29.46680.16611590.151227852944100

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