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Yorodumi- PDB-4ybr: Structure of Mycobacterium tuberculosis NadD in complex with NADP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ybr | |||||||||
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Title | Structure of Mycobacterium tuberculosis NadD in complex with NADP, P21212 | |||||||||
Components | Nicotinate-nucleotide adenylyltransferase | |||||||||
Keywords | TRANSFERASE / Rossman fold | |||||||||
Function / homology | Function and homology information nicotinate-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å | |||||||||
Authors | Korotkov, K.V. | |||||||||
Funding support | United States, 1items
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Citation | Journal: to be published Title: Structure of Mycobacterium tuberculosis NadD in complex with NADP, P21212 Authors: Korotkov, K.V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ybr.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ybr.ent.gz | 78 KB | Display | PDB format |
PDBx/mmJSON format | 4ybr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ybr_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4ybr_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4ybr_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 4ybr_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/4ybr ftp://data.pdbj.org/pub/pdb/validation_reports/yb/4ybr | HTTPS FTP |
-Related structure data
Related structure data | 5dasC 4s1oS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 22352.281 Da / Num. of mol.: 2 / Fragment: residues 3-200 / Mutation: C196R, C200T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: nadD, Rv2421c, MTCY428.26 / Plasmid: pRSF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: P9WJJ5, nicotinate-nucleotide adenylyltransferase |
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-Non-polymers , 5 types, 347 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE AUTHORS STATE THAT THE SEQUENCE IS MIS-ANNOTATED IN THE DATABASES. THE CORRECT START SEQUENCE ...THE AUTHORS STATE THAT THE SEQUENCE IS MIS-ANNOTATED IN THE DATABASES. THE CORRECT START SEQUENCE IS MHGRRLGVM WHICH WAS CONFIRMED EXPERIMENT |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.87 / Details: 0.1M HEPES pH 7.5, 1.26M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97903 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 9, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97903 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→70.71 Å / Num. all: 53894 / Num. obs: 53277 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 28.953 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.071 / Χ2: 1.021 / Net I/σ(I): 16.45 / Num. measured all: 295263 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4S1O Resolution: 1.65→70.71 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.2168 / WRfactor Rwork: 0.1873 / FOM work R set: 0.8446 / SU B: 2.137 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1005 / SU Rfree: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.45 Å2 / Biso mean: 25.641 Å2 / Biso min: 11.5 Å2
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Refinement step | Cycle: final / Resolution: 1.65→70.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.692 Å / Total num. of bins used: 20
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