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- PDB-2hbt: Crystal structure of HIF prolyl hydroxylase EGLN-1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2hbt
TitleCrystal structure of HIF prolyl hydroxylase EGLN-1 in complex with a biologically active inhibitor
ComponentsEgl nine homolog 1
KeywordsOXIDOREDUCTASE / prolyl hydroxylase / hypoxia inducible factor / HIF / EGLN / 2-oxoglutarate / oxygenase
Function / homology
Function and homology information


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 / 2-oxoglutarate-dependent dioxygenase activity ...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 / 2-oxoglutarate-dependent dioxygenase activity / cardiac muscle tissue morphogenesis / 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 / cytosol / cytoplasm
Similarity search - Function
Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Oxoglutarate/iron-dependent dioxygenase ...Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues. / q2cbj1_9rhob like domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Chem-UN9 / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å
AuthorsEvdokimov, A.G. / Walter, R.L. / Mekel, M. / Pokross, M.E. / Kawamoto, R. / Boyer, A.
CitationJournal: To be Published
Title: Crystal structure of HIF prolyl hydroxylase in complex with a biologically active inhibitor
Authors: Evdokimov, A.G. / Walter, R.L. / Mekel, M. / Pokross, M.E. / Kawamoto, R. / Boyer, A.
History
DepositionJun 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1693
Polymers27,8331
Non-polymers3372
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.166, 111.166, 40.229
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Egl nine homolog 1 / Hypoxia-inducible factor prolyl hydroxylase 2 / HIF-prolyl hydroxylase 2 / HIF-PH2 / HPH-2 / Prolyl ...Hypoxia-inducible factor prolyl hydroxylase 2 / HIF-prolyl hydroxylase 2 / HIF-PH2 / HPH-2 / Prolyl hydroxylase domain-containing protein 2 / PHD2 / SM-20


Mass: 27832.674 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGLN1 / Plasmid: pET45-DEST / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)*
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 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-UN9 / N-[(1-CHLORO-4-HYDROXYISOQUINOLIN-3-YL)CARBONYL]GLYCINE


Mass: 280.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9ClN2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 200-300 mM (NH4)2SO4, 100 mM NaOAc pH 4.8-5.4, 22-25% PEG-4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 8, 2005
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 36629 / Num. obs: 36629 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.019 / Net I/σ(I): 28.8
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 4.3 / Num. unique all: 6117 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345data collection
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.292 / SU ML: 0.087 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.096 / ESU R Free: 0.096 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1814 5 %RANDOM
Rwork0.213 ---
all0.214 36503 --
obs0.21 36503 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.705 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.07 Å20 Å2
2---0.15 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1845 0 20 140 2005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221916
X-RAY DIFFRACTIONr_bond_other_d0.0010.021749
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9742601
X-RAY DIFFRACTIONr_angle_other_deg0.69534090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.275248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55323.37189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.58215351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5581516
X-RAY DIFFRACTIONr_chiral_restr0.1180.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022147
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02406
X-RAY DIFFRACTIONr_nbd_refined0.2670.2428
X-RAY DIFFRACTIONr_nbd_other0.2480.21867
X-RAY DIFFRACTIONr_nbtor_refined0.1970.2904
X-RAY DIFFRACTIONr_nbtor_other0.0950.21104
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2119
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3290.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4420.215
X-RAY DIFFRACTIONr_mcbond_it2.9371.51493
X-RAY DIFFRACTIONr_mcbond_other1.0791.5476
X-RAY DIFFRACTIONr_mcangle_it3.22821852
X-RAY DIFFRACTIONr_scbond_it4.6383918
X-RAY DIFFRACTIONr_scangle_it5.774.5736
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 119 -
Rwork0.308 2581 -
obs-2700 96.74 %

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