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- PDB-6yw0: Lysine-N,N-Dimethylated HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in... -

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Basic information

Entry
Database: PDB / ID: 6yw0
TitleLysine-N,N-Dimethylated HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with BB-287
ComponentsEgl nine homolog 1
KeywordsOXIDOREDUCTASE / NON-HEME DIOXYGENASE / IRON / 2-OXOGLUTARATE / HYPOXIA-INDUCIBLE FACTOR / HIF / HIF PROLYL HYDROXYLASE DOMAIN 2 / PHD2 / EGLN1 / OXYGENASE / HYPOXIA / DNA-BINDING / METAL-BINDING / TRANSCRIPTION / HELIX-LOOP-HELIX-BETA / DSBH / FACIAL TRIAD / CYTOPLASM / TRANSCRIPTION/EPIGENETIC REGULATION / SIGNALING / DEVELOPMENT / CELL STRUCTURE / BETA-HYDROXYLATION / TRANSCRIPTION ACTIVATOR/INHIBITOR / UBL CONJUGATION / POLYMORPHISM / VITAMIN C / ZINC-FINGER / FAMILIAL ERYTHROCYTOSIS / BREAST CANCER / TRANSCRIPTION COMPLEX
Function / homology
Function and homology information


peptidyl-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / negative regulation of hypoxia-inducible factor-1alpha signaling pathway / peptidyl-proline dioxygenase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / regulation of modification of postsynaptic structure / labyrinthine layer development / 2-oxoglutarate-dependent dioxygenase activity ...peptidyl-proline 4-dioxygenase activity / hypoxia-inducible factor-proline dioxygenase activity / hypoxia-inducible factor-proline dioxygenase / negative regulation of hypoxia-inducible factor-1alpha signaling pathway / peptidyl-proline dioxygenase activity / regulation protein catabolic process at postsynapse / intracellular oxygen homeostasis / regulation of modification of postsynaptic structure / labyrinthine layer development / 2-oxoglutarate-dependent dioxygenase activity / heart trabecula formation / cardiac muscle tissue morphogenesis / L-ascorbic acid binding / response to nitric oxide / ventricular septum morphogenesis / enzyme inhibitor activity / regulation of angiogenesis / regulation of neuron apoptotic process / ferrous iron binding / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cellular response to hypoxia / intracellular iron ion homeostasis / response to hypoxia / postsynaptic density / intracellular membrane-bounded organelle / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytoplasm / cytosol
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. / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile.
Similarity search - Domain/homology
4-(isoquinolin-3-ylamino)-4-oxobutanoic acid / BICARBONATE ION / : / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChowdhury, R. / Schofield, C.J.
Citation
Journal: Sci Rep / Year: 2020
Title: Use of cyclic peptides to induce crystallization: case study with prolyl hydroxylase domain 2.
Authors: Chowdhury, R. / Abboud, M.I. / McAllister, T.E. / Banerji, B. / Bhushan, B. / Sorensen, J.L. / Kawamura, A. / Schofield, C.J.
#1: Journal: ACS Chem. Biol. / Year: 2013
Title: Selective small molecule probes for the hypoxia inducible factor (HIF) prolyl hydroxylases.
Authors: Chowdhury, R. / Candela-Lena, J.I. / Chan, M.C. / Greenald, D.J. / Yeoh, K.K. / Tian, Y.M. / McDonough, M.A. / Tumber, A. / Rose, N.R. / Conejo-Garcia, A. / Demetriades, M. / Mathavan, S. / ...Authors: Chowdhury, R. / Candela-Lena, J.I. / Chan, M.C. / Greenald, D.J. / Yeoh, K.K. / Tian, Y.M. / McDonough, M.A. / Tumber, A. / Rose, N.R. / Conejo-Garcia, A. / Demetriades, M. / Mathavan, S. / Kawamura, A. / Lee, M.K. / van Eeden, F. / Pugh, C.W. / Ratcliffe, P.J. / Schofield, C.J.
History
DepositionApr 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.B_iso_Wilson_estimate / _reflns_shell.meanI_over_sigI_obs
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0264
Polymers28,6651
Non-polymers3613
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-13 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.927, 110.927, 39.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 / HPH-2 / Prolyl hydroxylase domain-containing ...Hypoxia-inducible factor prolyl hydroxylase 2 / HPH-2 / Prolyl hydroxylase domain-containing protein 2 / PHD2 / SM-20


Mass: 28664.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CATALYTIC DOMAIN (aa 181-426) / Source: (gene. exp.) Homo sapiens (human) / Gene: EGLN1, C1orf12, PNAS-118, PNAS-137 / Plasmid: PET28A(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9GZT9, hypoxia-inducible factor-proline dioxygenase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-2JP / 4-(isoquinolin-3-ylamino)-4-oxobutanoic acid


Mass: 244.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.09 Å3/Da / Density % sol: 60.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Sample: 18 mg/mL PHD2-Me + 1 mM FeSO4 + 2 mM compound; Reservoir: 1.7% polyethylene glycol 400, 15% glycerol, 1.7 M ammonium sulphate and 0.085 M HEPES-Na pH 7.5; Sitting drop (2 uL), protein-to-well ratio, 1:1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 1, 2006
Details: PT COATED MIRRORS IN A KIRKPATRICK-BAEZ (KB) GEOMETRY
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.2→36.309 Å / Num. all: 14427 / Num. obs: 14427 / % possible obs: 99.9 % / Redundancy: 20.3 % / Biso Wilson estimate: 41 Å2 / Rpim(I) all: 0.04 / Rrim(I) all: 0.182 / Rsym value: 0.177 / Net I/av σ(I): 3.9 / Net I/σ(I): 19.1 / Num. measured all: 293273
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.3220.82.0371.744321420800.4552.0882.0372.1100
2.32-2.4621.11.5410.54148819650.3411.5781.5412.9100
2.46-2.63210.9960.73913318610.2211.0210.9964.4100
2.63-2.84210.6481.13666917480.1440.6640.6486.6100
2.84-3.1120.90.3182.33329815930.0710.3260.31812.4100
3.11-3.4820.70.1654.52996714480.0370.1690.16521100
3.48-4.0219.80.10172560912930.0230.1030.10132.3100
4.02-4.9219.30.06410.32115410940.0150.0660.06450.2100
4.92-6.96180.0610.2154658590.0150.0620.0662.9100
6.96-36.309150.03814.472764860.0110.040.03891.398.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G19

2g19


Resolution: 2.2→32.022 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2208 723 5.02 %
Rwork0.1923 --
obs0.1937 14413 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / Bsol: 63.5 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso max: 242.2 Å2 / Biso mean: 71.7747 Å2 / Biso min: 28.33 Å2
Refinement stepCycle: final / Resolution: 2.2→32.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 35 63 1841
Biso mean--50.19 57.82 -
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_d0.0040.0341819
X-RAY DIFFRACTIONf_angle_d0.8518.9972464
X-RAY DIFFRACTIONf_dihedral_angle_d9.594179.9511389
X-RAY DIFFRACTIONf_chiral_restr0.0510.185257
X-RAY DIFFRACTIONf_plane_restr0.0050.04314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2-2.36970.35911390.31952698
2.3697-2.60810.32091440.27712709
2.6081-2.98530.25221450.23822721
2.9853-3.76020.21491480.18982744
3.7602-32.0220.17671470.14772818
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1639-0.1818-0.17390.2990.18390.1411-0.0248-0.0344-0.168-0.0514-0.0067-1.2790.1647-0.19880.05120.55240.0898-0.16620.6637-0.00140.828516.690233.81491.4451
20.64560.13740.83260.19780.22661.16610.34580.0598-0.78040.2980.2588-0.54670.58020.58720.34790.71640.1353-0.12790.4186-0.02810.59947.758232.74210.0433
30.26970.0693-0.03290.1231-0.0672-0.00620.3002-0.2508-0.75210.8629-0.38710.63160.7511-0.2743-0.00410.8737-0.1180.09010.52510.10320.7243-8.728334.038211.7088
40.32540.124-0.28510.591-0.20660.5366-0.0736-0.43810.48070.4138-0.31350.9955-0.0411-0.4346-0.07640.52030.028-0.05860.448-0.06030.7506-14.026247.79492.5415
50.3941-0.18760.13130.58740.4230.43820.1481-0.5015-0.13350.970.0604-0.66990.53460.03710.06640.70490.1029-0.22420.54880.03180.46837.440240.237611.4301
60.2414-0.0321-0.14730.059-0.03070.177-0.3445-0.2177-0.2833-0.7222-0.4864-0.9504-0.4841-0.0662-0.01570.5808-0.0883-0.06250.4984-0.01450.935818.483147.47452.1786
70.4851-0.1584-0.51270.6353-0.14290.4888-0.0645-0.2983-0.05590.39320.19710.5011-0.1774-0.01390.01710.4583-0.0332-0.07780.3927-0.02510.4825-5.564144.68732.9542
81.1539-0.2475-0.26410.83990.50740.2554-0.04470.12260.8843-0.8727-0.06240.4726-0.2961-0.06680.0750.5636-0.0025-0.19760.36450.05730.3735-1.241249.1111-8.7077
90.4522-0.5312-0.26550.40710.11250.94760.05660.0732-0.2109-0.22160.14640.17650.44980.19840.29020.487-0.0189-0.19980.29350.0590.4619-0.7436.70080.396
100.222-0.1108-0.08150.17260.24440.10480.1790.6725-0.8566-0.78260.0684-0.35490.16420.260.04140.7914-0.0743-0.05010.4289-0.07170.5328-0.169236.2719-12.4192
110.1621-0.2226-0.02230.28850.00210.0294-0.18480.6358-1.1591-0.1126-0.0739-0.09340.3435-0.0630.05960.6242-0.0148-0.07710.4037-0.08580.46480.589932.1402-6.9602
120.2666-0.00120.01750.10550.09860.0420.31770.08-0.0672-0.3862-0.1955-0.06380.344-0.09170.01420.48410.0586-0.02640.3252-0.02960.38777.555842.5556-5.0972
130.43750.12610.00410.368-0.0855-0.03170.14411.1288-0.1396-1.2855-0.17530.1640.23270.2515-0.4050.5876-0.1465-0.41830.3268-0.11060.4569-5.759539.147-10.0554
140.2111-0.3572-0.16730.32230.2211-0.0790.3170.0047-0.25470.3225-0.1506-0.20240.16250.1278-0.00010.4334-0.0448-0.08710.2957-0.00070.38740.300543.82992.3233
150.03130.04950.01370.09430.00840.0796-0.3631-0.1256-0.2911-0.29910.1457-0.2197-0.1863-0.36040.00010.4658-0.0731-0.05820.5134-0.06020.616311.086161.17240.7369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 188:204)A188 - 204
2X-RAY DIFFRACTION2(chain A and resid 205:215)A205 - 215
3X-RAY DIFFRACTION3(chain A and resid 216:232)A216 - 232
4X-RAY DIFFRACTION4(chain A and resid 233:266)A233 - 266
5X-RAY DIFFRACTION5(chain A and resid 267:283)A267 - 283
6X-RAY DIFFRACTION6(chain A and resid 284:293)A284 - 293
7X-RAY DIFFRACTION7(chain A and resid 294:306)A294 - 306
8X-RAY DIFFRACTION8(chain A and resid 307:320)A307 - 320
9X-RAY DIFFRACTION9(chain A and resid 321:335)A321 - 335
10X-RAY DIFFRACTION10(chain A and resid 336:350)A336 - 350
11X-RAY DIFFRACTION11(chain A and resid 351:361)A351 - 361
12X-RAY DIFFRACTION12(chain A and resid 362:371)A362 - 371
13X-RAY DIFFRACTION13(chain A and resid 372:381)A372 - 381
14X-RAY DIFFRACTION14(chain A and resid 382:392)A382 - 392
15X-RAY DIFFRACTION15(chain A and resid 393:403)A393 - 403

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