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Yorodumi- PDB-6x3b: Structure of RMD from Pseudomonas aeruginosa complexed with NADPH -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x3b | ||||||
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Title | Structure of RMD from Pseudomonas aeruginosa complexed with NADPH | ||||||
Components | GDP-6-deoxy-D-mannose reductase | ||||||
Keywords | OXIDOREDUCTASE / O-antigen / Lipopolysaccharide / GDP-rhamnose / NADPH / Pseudomonas | ||||||
Function / homology | GDP-mannose 4,6-dehydratase activity / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / NAD(P)-binding domain superfamily / Chem-NDP / NITRATE ION / PYROPHOSPHATE 2- / GDP-6-deoxy-D-mannose reductase Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Cook, P.D. / Nicholson, B.E. / McHugh, C.S. | ||||||
Citation | Journal: To Be Published Title: X-ray crystallographic structure of RMD, the reductase involved in GDP-d-rhamnose production Authors: Nicholson, B.E. / McHugh, C.S. / Cook, P.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6x3b.cif.gz | 255.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6x3b.ent.gz | 204.1 KB | Display | PDB format |
PDBx/mmJSON format | 6x3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x3b_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 6x3b_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6x3b_validation.xml.gz | 48.1 KB | Display | |
Data in CIF | 6x3b_validation.cif.gz | 67.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/6x3b ftp://data.pdbj.org/pub/pdb/validation_reports/x3/6x3b | HTTPS FTP |
-Related structure data
Related structure data | 2pk3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36296.223 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: CGU42_28985, DZ962_06890, EQH76_14905, F3H14_30110 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A071L2P8 #2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-NO3 / | #4: Chemical | ChemComp-POP / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.39 Å3/Da / Density % sol: 48.51 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 10% PEG 3350, 100 mM lithium nitrate, 10 mM HEPES, 25 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å | ||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 21, 2014 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.91→34.03 Å / Num. obs: 105890 / % possible obs: 99.1 % / Redundancy: 5 % / Biso Wilson estimate: 26.57 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.049 / Rrim(I) all: 0.111 / Net I/σ(I): 8.5 / Num. measured all: 534372 / Scaling rejects: 287 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2pk3 Resolution: 1.91→34.028 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.68 Å2 / Biso mean: 35.3508 Å2 / Biso min: 11.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.91→34.028 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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