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- PDB-6yvz: HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with bicyclic J... -

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Basic information

Entry
Database: PDB / ID: 6yvz
TitleHIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with bicyclic JLS-367
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 / regulation of angiogenesis / enzyme inhibitor activity / 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 / 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. / 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
BICARBONATE ION / : / Chem-PW8 / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsChowdhury, R. / Sorensen, J.L. / 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 24, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)28,5364
Polymers28,0971
Non-polymers4393
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-6 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.880, 109.880, 39.080
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: 28096.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CATALYTIC DOMAIN (RESIDUES 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PW8 / 4-[(5-bromanylisoquinolin-3-yl)amino]-4-oxidanylidene-butanoic acid


Mass: 323.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H11BrN2O3 / 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.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sample: (~20 mg/ml-1 PHD2 + 1 mM MnCl2 + 2 mM compound); Reservoir: 1.6-2.0 M (NH4)2SO4, 2-8% dioxane, 0.1 M MES-Na pH 6.5, and 1 mM MnCl2; Sitting drop (2 ul), protein-to-well ratio, 1:1, 293K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 5, 2015 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.91→36.15 Å / Num. obs: 21231 / % possible obs: 99.9 % / Redundancy: 11.4 % / Biso Wilson estimate: 37.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.031 / Rrim(I) all: 0.103 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.91-1.96121.3362.115870.6620.4031.396100
8.54-36.1510.20.0592660.9980.0190.06298.4

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G19

2g19


Resolution: 1.91→36.15 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2035 1064 5.01 %
Rwork0.1665 --
obs0.1684 21221 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / Bsol: 65.4 Å2 / ksol: 0.46 e/Å3
Displacement parametersBiso max: 212.46 Å2 / Biso mean: 57.7648 Å2 / Biso min: 24.8 Å2
Refinement stepCycle: final / Resolution: 1.91→36.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 35 89 1843
Biso mean--70.32 58.78 -
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_d0.0140.1021809
X-RAY DIFFRACTIONf_angle_d1.1739.5242453
X-RAY DIFFRACTIONf_dihedral_angle_d15.513179.5681062
X-RAY DIFFRACTIONf_chiral_restr0.0750.308260
X-RAY DIFFRACTIONf_plane_restr0.0090.046320
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9101-1.9970.31221500.26592472
1.997-2.10230.25371410.21862490
2.1023-2.2340.21141410.18652491
2.234-2.40640.1891290.17112498
2.4064-2.64860.20181230.1862530
2.6486-3.03160.19381130.17642535
3.0316-3.81890.18971320.15412531
3.8189-36.150.20231350.14922610
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)
10.52870.5430.01430.48460.07150.0798-0.12930.1772-0.8306-0.0423-0.0336-0.0560.687-0.21610.02560.53920.0470.00510.37990.10880.445837.39072.61513.8243
20.4306-0.114-0.09620.183-0.16550.3184-0.25080.2104-0.89010.2982-0.12360.18961.074-0.24220.00950.4294-0.11990.01520.34510.07690.352131.99919.44522.3098
30.61630.3150.1830.17130.0190.19750.0506-0.6790.520.4996-0.23380.9318-0.0592-0.6968-0.02780.4662-0.01330.10820.62510.06750.457225.058424.712713.9236
40.43410.56560.15860.76910.64590.4409-0.306-0.1440.41870.31150.01770.1986-0.73470.0017-0.00010.53280.0027-0.05940.40060.01470.484133.999735.92124.4317
50.21830.05980.30280.13110.17670.16340.0997-0.1199-0.17560.7234-0.1887-0.57320.2175-0.2870.00010.5395-0.0088-0.04440.38550.0920.409938.183713.642913.7211
60.11670.01010.06980.1066-0.0168-0.0044-0.61690.9852-0.9078-0.12611.19590.17590.5310.679-0.00040.5497-0.0413-0.09120.62310.02860.707449.80387.9084.3711
70.1461-0.00330.0160.34360.37950.16960.2922-0.0117-0.07530.0811-0.05110.2462-0.0724-0.0555-0.00030.3480.0199-0.04210.36670.06170.402935.391126.85524.9917
80.41520.1830.16150.4603-0.05410.1318-0.18950.16090.828-0.068-0.12-0.6512-0.26640.155-0.00490.27450.0066-0.02650.40610.13350.41841.652725.3398-6.417
90.14790.4029-0.06951.01170.0530.7488-0.05370.0604-0.22450.13360.00420.07150.2778-0.0713-0.00010.2611-0.02160.01480.31260.09970.331231.851418.74212.5202
100.30420.50120.33880.58410.51370.3304-0.15350.4727-0.6226-0.2133-0.06710.29160.0875-0.0311-0.00030.31560.0004-0.02130.44330.0120.382530.930118.4433-10.1978
110.34880.05110.28760.2324-0.08470.1869-0.36480.2505-0.4865-0.1025-0.15480.20030.7594-0.14110.00080.4148-0.03930.00270.47210.05020.347228.270215.2467-5.4419
120.22840.0060.2325-0.03420.07930.2244-0.1255-0.2162-0.0105-0.13590.0503-0.06930.30250.21740.00030.3215-0.02590.01950.32450.06530.349540.256914.506-2.782
130.21440.24960.17450.18010.18960.1230.2109-0.0283-0.2112-0.5633-0.12640.3126-0.0365-0.12110.00010.32050.0335-0.04530.37530.08070.351830.831424.1817-7.8881
140.41570.90050.36681.42830.36730.3916-0.1371-0.3706-0.39310.17730.20010.08030.0683-0.08780.00020.26930.0083-0.04010.34680.06750.3237.716721.46054.5771
150.08260.10040.07370.11550.0750.1091-0.1131.06560.4798-0.02450.04120.0913-0.0545-0.18990.00080.32480.0519-0.08310.46060.07530.592558.125320.82631.9652
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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