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- PDB-7rkb: Crystal Structure of Putative Pterin Binding Protein (PruR) from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rkb | ||||||
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Title | Crystal Structure of Putative Pterin Binding Protein (PruR) from Klebsiella pneumoniae in Complex with Neopterin | ||||||
![]() | Pterin Binding Protein | ||||||
![]() | PTERIN BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / PruR | ||||||
Function / homology | Oxidoreductase, molybdopterin-binding domain / Oxidoreductase molybdopterin binding domain / Oxidoreductase, molybdopterin-binding domain superfamily / L-NEOPTERIN / Molybdopterin-dependent oxidoreductase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of Putative Pterin Binding Protein (PruR) from Klebsiella pneumoniae in Complex with Neopterin. Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Satchell, K.J.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.3 KB | Display | ![]() |
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PDB format | ![]() | 56.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 698.4 KB | Display | ![]() |
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Full document | ![]() | 699.5 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 10.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 17068.654 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: RJA_09115 / Plasmid: pMCSG53 / Production host: ![]() ![]() | ||||||
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#2: Chemical | ChemComp-NEU / | ||||||
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.53 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 8.0 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris, pH 8.3, 2 mM Neopterin against Classics II screen G5 (0.2 M lithium sulfate, 0.1 M Tris, pH 8.5, 25% w/v PEG3350) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2019 / Details: Be |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 5990 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Biso Wilson estimate: 57 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.045 / Rrim(I) all: 0.163 / Rsym value: 0.157 / Χ2: 1.261 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 14.2 % / Rmerge(I) obs: 1.675 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 298 / CC1/2: 0.709 / CC star: 0.911 / Rpim(I) all: 0.461 / Rsym value: 1.675 / Χ2: 1.004 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 175.73 Å2 / Biso mean: 68.845 Å2 / Biso min: 39.13 Å2
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Refinement step | Cycle: final / Resolution: 2.5→29.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.502→2.566 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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