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Open data
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Basic information
Entry | Database: PDB / ID: 2y33 | ||||||
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Title | S-nitrosylated PHD2 (GSNO soaked) in complex with Zn(II) and UN9 | ||||||
![]() | EGL NINE HOMOLOG 1 | ||||||
![]() | OXIDOREDUCTASE / NON-HEME / TRANSCRIPTION AND EPIGENETIC REGULATION | ||||||
Function / homology | ![]() hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / labyrinthine layer development / cardiac muscle tissue morphogenesis ...hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / peptidyl-proline 4-dioxygenase activity / peptidyl-proline dioxygenase activity / peptidyl-proline hydroxylation to 4-hydroxy-L-proline / negative regulation of cyclic-nucleotide phosphodiesterase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / labyrinthine layer development / cardiac muscle tissue morphogenesis / 2-oxoglutarate-dependent dioxygenase activity / heart trabecula formation / regulation of modification of postsynaptic structure / L-ascorbic acid binding / response to nitric oxide / ventricular septum morphogenesis / regulation of angiogenesis / ferrous iron binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / negative regulation of DNA-binding transcription factor activity / cellular response to hypoxia / intracellular iron ion homeostasis / postsynaptic density / response to hypoxia / intracellular membrane-bounded organelle / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chowdhury, R. / Clifton, I.J. / Schofield, C.J. | ||||||
![]() | ![]() Title: Studies on the Reaction of Nitric Oxide with the Hypoxia-Inducible Factor Prolyl Hydroxylase Domain 2 (Egln1) Authors: Chowdhury, R. / Flashman, E. / Mecinovic, J. / Kramer, H.B. / Kessler, B.M. / Frapart, Y.M. / Boucher, J.-L. / Clifton, I.J. / McDonough, M.A. / Schofield, C.J. #1: ![]() Title: Structural Basis for Binding of Hypoxia-Inducible Factor to the Oxygen-Sensing Prolyl Hydroxylases. Authors: Chowdhury, R. / McDonough, M.A. / Mecinovic, J. / Loenarz, C. / Flashman, E. / Hewitson, K.S. / Domene, C. / Schofield, C.J. #2: ![]() Title: Cellular Oxygen Sensing: Crystal Structure of Hypoxia-Inducible Factor Prolyl Hydroxylase (Phd2). Authors: McDonough, M.A. / Li, V. / Flashman, E. / Chowdhury, R. / Mohr, C. / Lienard, B.M.R. / Zondlo, J. / Oldham, N.J. / Clifton, I.J. / Lewis, J. / Mcneill, L.A. / Kurzeja, R.J.M. / Hewitson, K.S. ...Authors: McDonough, M.A. / Li, V. / Flashman, E. / Chowdhury, R. / Mohr, C. / Lienard, B.M.R. / Zondlo, J. / Oldham, N.J. / Clifton, I.J. / Lewis, J. / Mcneill, L.A. / Kurzeja, R.J.M. / Hewitson, K.S. / Yang, E. / Jordan, S. / Syed, R.S. / Schofield, C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.4 KB | Display | ![]() |
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PDB format | ![]() | 43.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 727.4 KB | Display | ![]() |
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Full document | ![]() | 729.7 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 16.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y34C ![]() 2g19S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28125.939 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 181-426 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9GZT9, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-UN9 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.89 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 8.5 Details: APPROX. 20 MG/ML APO-PHD2, 1MM ZN-ACETATE, 1MM FG2, VAPOR DIFFUSION, SITTING DROP, 30% PEG 4000 (W/V), 0.2M SODIUM ACETATE, 0.1 M TRIS-HCL PH 8.5; PRE-GROWN CRYSTALS WERE SOAKED WITH 50 MM GSNO FOR 12 HR. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9695 Å / Relative weight: 1 |
Reflection | Resolution: 2→37.19 Å / Num. obs: 19446 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5.1 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.2 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2G19 Resolution: 2→36.35 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 158464.65 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: TREATMENT OF PHD2 WITH GSNO RESULTED IN S-NITROSYLATION OF CYS 302, WHICH WAS REFINED AS R-S-NO. HOWEVER, THE DIHEDRAL ANGLE FOR THE C-S-N-O GROUP SUGGESTS THAT THE MODIFIED RESIDUE MAY, AT ...Details: TREATMENT OF PHD2 WITH GSNO RESULTED IN S-NITROSYLATION OF CYS 302, WHICH WAS REFINED AS R-S-NO. HOWEVER, THE DIHEDRAL ANGLE FOR THE C-S-N-O GROUP SUGGESTS THAT THE MODIFIED RESIDUE MAY, AT LEAST IN PART, BE THE R-S-N*-OH, WHICH IS A PROPOSED REACTION INTERMEDIATE OF NO WITH THIOLS, OR THE O- CENTRED THIONITROXIDE RADICAL R-S-NH-O*. OTHER POTENTIAL FORMS SUCH AS R-S-NH-OH MAY ALSO RESULT FROM PARTIAL REDUCTION OF R-S- NO DURING DATA COLLECTION.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 62.2681 Å2 / ksol: 0.384767 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→36.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.11 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 7
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Xplor file |
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