+
Open data
-
Basic information
Entry | Database: PDB / ID: 2y34 | ||||||
---|---|---|---|---|---|---|---|
Title | S-nitrosylated PHD2 (NO exposed) in complex with Fe(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. / McDonough, M.A. / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 63.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 44.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 991.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 995.9 KB | Display | |
Data in XML | ![]() | 12.2 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y33C ![]() 2g19S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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 | ||
---|---|---|---|
#2: Chemical | ChemComp-FE2 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.32 % / Description: NONE |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6M AMMONIUM SULFATE, 4% DIOXANE, 0.1M MES PH6.5, VAPOR DIFFUSION, HANGING DROP, PRE-GROWN CRYSTALS WERE EXPOSED TO NITRIC OXIDE SATURATED SOLUTION (1 ML, DENSITY 1.34 G/L) FOR AN HOUR. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 13, 2005 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→27.58 Å / Num. obs: 18814 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.42 |
Reflection shell | Resolution: 2.01→2.08 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.07 / % possible all: 94.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2G19 Resolution: 2.01→27.58 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 108842.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 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.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.2117 Å2 / ksol: 0.347596 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→27.58 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.01→2.08 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|