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Yorodumi- PDB-4xwy: Crystal structure of human sepiapterin reductase in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xwy | ||||||
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Title | Crystal structure of human sepiapterin reductase in complex with an N-acetylserotinin analogue | ||||||
Components | Sepiapterin reductase | ||||||
Keywords | OXIDOREDUCTASE / inhibitor / complex | ||||||
Function / homology | Function and homology information sepiapterin reductase (L-erythro-7,8-dihydrobiopterin-forming) / sepiapterin reductase (NADP+) activity / aldo-keto reductase (NADPH) activity / tetrahydrobiopterin biosynthetic process / eNOS activation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / nitric oxide biosynthetic process / NADP binding / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å | ||||||
Authors | Johnsson, K. / Hovius, R. / Gorszka, K.I. / Pojer, F. | ||||||
Citation | Journal: Neuron / Year: 2015 Title: Reduction of Neuropathic and Inflammatory Pain through Inhibition of the Tetrahydrobiopterin Pathway. Authors: Latremoliere, A. / Latini, A. / Andrews, N. / Cronin, S.J. / Fujita, M. / Gorska, K. / Hovius, R. / Romero, C. / Chuaiphichai, S. / Painter, M. / Miracca, G. / Babaniyi, O. / Remor, A.P. / ...Authors: Latremoliere, A. / Latini, A. / Andrews, N. / Cronin, S.J. / Fujita, M. / Gorska, K. / Hovius, R. / Romero, C. / Chuaiphichai, S. / Painter, M. / Miracca, G. / Babaniyi, O. / Remor, A.P. / Duong, K. / Riva, P. / Barrett, L.B. / Ferreiros, N. / Naylor, A. / Penninger, J.M. / Tegeder, I. / Zhong, J. / Blagg, J. / Channon, K.M. / Johnsson, K. / Costigan, M. / Woolf, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xwy.cif.gz | 216.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xwy.ent.gz | 173.8 KB | Display | PDB format |
PDBx/mmJSON format | 4xwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xwy_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 4xwy_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 4xwy_validation.xml.gz | 41.9 KB | Display | |
Data in CIF | 4xwy_validation.cif.gz | 56 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xw/4xwy ftp://data.pdbj.org/pub/pdb/validation_reports/xw/4xwy | HTTPS FTP |
-Related structure data
Related structure data | 4hwkS 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: 29891.414 Da / Num. of mol.: 4 / Fragment: residues 15-275 Source method: isolated from a genetically manipulated source Details: The N-termius" MHHHHHHENLYFQG" was added for purification M15 is original start codon of the protein residues 1-17 "MHHHHHHENLYFQGMEG" and 275 "K" are not resolved in the structure Source: (gene. exp.) Homo sapiens (human) / Gene: SPR / Plasmid: pET9a / Production host: Escherichia coli bl21(de3) (bacteria) References: UniProt: P35270, sepiapterin reductase (L-erythro-7,8-dihydrobiopterin-forming) #2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-43O / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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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: 4.58 Å3/Da / Density % sol: 73.12 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2% W/V PEG1000, 2.5% V/V glycerol, 1.7 M Ammonium sulfate, 0.1 M Hepes PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→125.435 Å / Num. all: 89220 / Num. obs: 89220 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 55.8 Å2 / Rpim(I) all: 0.03 / Rrim(I) all: 0.1 / Rsym value: 0.096 / Net I/av σ(I): 6.536 / Net I/σ(I): 15.8 / Num. measured all: 998773 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.555
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4HWK Resolution: 2.35→125.435 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.1983 / WRfactor Rwork: 0.1699 / FOM work R set: 0.8433 / SU B: 5.423 / SU ML: 0.126 / SU R Cruickshank DPI: 0.1789 / SU Rfree: 0.1629 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.163 / 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: 200.07 Å2 / Biso mean: 48.374 Å2 / Biso min: 21.32 Å2
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Refine analyze | Luzzati coordinate error obs: 0.296 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.35→125.435 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Total num. of bins used: 20
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