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- PDB-6yvw: HIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with monocyclic... -

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Basic information

Entry
Database: PDB / ID: 6yvw
TitleHIF prolyl hydroxylase 2 (PHD2/ EGLN1) in complex with monocyclic BB-328
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 / 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
: / Chem-PW5 / Egl nine homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsChowdhury, R. / Banerji, B. / 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 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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

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Assembly

Deposited unit
A: Egl nine homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5464
Polymers28,0971
Non-polymers4493
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-15 kcal/mol
Surface area11490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.175, 110.175, 39.791
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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-PW5 / 4-[(5-bromanyl-4,6-dimethyl-pyridin-2-yl)amino]-4-oxidanylidene-butanoic acid


Mass: 301.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13BrN2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.79 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Sample: (20 mg/ml PHD2 + 1 mM FeSO4 + 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 FeSO4; Hanging 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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 25, 2011 / Details: VARIMAX HF
RadiationMonochromator: CONFOCAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 19800 / % possible obs: 99.8 % / Redundancy: 7.8 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.092 / Χ2: 1.254 / Net I/σ(I): 18.77
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsΧ2% possible all
1.97-27.20.9152.389681.66699.6
2-2.047.30.8439661.569100
2.04-2.087.40.8249891.573100
2.08-2.127.60.8439931.51399.7
2.12-2.177.80.8689781.572100
2.17-2.227.80.7859931.46599.9
2.22-2.277.90.5539621.333100
2.27-2.347.70.5429941.36100
2.34-2.47.80.519721.35499.9
2.4-2.487.60.4469981.269100
2.48-2.577.70.3559731.154100
2.57-2.677.80.2879991.11199.8
2.67-2.880.2019890.934100
2.8-2.948.30.1289940.989100
2.94-3.138.30.0999920.966100
3.13-3.378.20.0799951.213100
3.37-3.718.10.0639931.12899.9
3.71-4.247.90.0510150.98199.9
4.24-5.358.10.04410051.046100
5.35-507.70.04110321.08597

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G19

2g19


Resolution: 1.97→18.448 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2081 1001 5.09 %
Rwork0.187 --
obs0.1881 19658 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT MODEL / Bsol: 50.8 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso max: 139 Å2 / Biso mean: 59.1114 Å2 / Biso min: 26.95 Å2
Refinement stepCycle: final / Resolution: 1.97→18.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1727 0 44 122 1893
Biso mean--83.18 54.43 -
Num. residues----222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_d0.0170.1351865
X-RAY DIFFRACTIONf_angle_d1.43911.9172534
X-RAY DIFFRACTIONf_dihedral_angle_d16.605179.8141103
X-RAY DIFFRACTIONf_chiral_restr0.0740.256266
X-RAY DIFFRACTIONf_plane_restr0.0110.05337
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.97-2.07380.30731380.30632644100
2.0738-2.20350.31911540.27772644100
2.2035-2.37330.271410.25572640100
2.3733-2.61150.30621290.2697263198
2.6115-2.98810.24771390.20522674100
2.9881-3.75940.19351590.16322658100
3.7594-18.4480.15321410.14312766100
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)
10.29090.3309-0.18180.7694-0.50150.302-0.0796-0.25060.92360.25440.23780.3443-0.16580.01860.13020.49950.04030.05250.366-0.15970.7961-37.386-2.57851.2381
20.5991-0.0987-0.78890.45480.03430.83990.5442-0.28421.4922-0.04670.2948-0.2335-1.13490.22930.14460.4217-0.19180.06210.4361-0.24420.6666-31.6048-9.66750.0899
30.63520.2250.08610.0691-0.11280.43110.1291-1.5118-0.34430.4141-0.2981-0.62070.07750.4828-0.04230.40870.0205-0.10530.8284-0.15590.4176-25.0419-24.504911.6828
41.95150.2162-0.3330.7387-0.76121.435-0.0966-0.3194-0.6893-0.10780.0813-0.2610.2512-0.04180.11650.4245-0.020.01850.49380.02380.4819-34.0174-36.26561.8562
50.64130.4669-0.3740.3106-0.22820.3508-0.0868-1.34460.95210.3310.17730.0348-0.27970.08110.09250.45580.00640.02370.5905-0.26760.4128-38.1911-13.766911.7279
60.25440.7517-0.85552.3288-2.71584.9159-0.4302-0.1441.4729-0.21940.84640.30330.5226-0.99420.10460.20810.03040.04710.3743-0.04950.8675-49.8771-8.12311.861
70.35330.4693-0.36780.7211-0.59370.25650.2896-0.1204-0.1561-0.0801-0.1393-0.1066-0.1466-0.0144-0.00050.29090.0296-0.00760.4078-0.03230.3181-35.458-26.95462.482
80.32570.5660.18020.85590.44420.2479-0.13770.4644-0.9162-0.2548-0.07510.6850.03260.0251-0.00650.34120.0101-0.05510.457-0.0960.3608-41.7501-25.5337-8.8594
90.18120.3533-0.4331.3099-0.36091.0209-0.00830.13070.3925-0.04530.1387-0.176-0.15960.30640.23590.269-0.04130.02090.4007-0.17410.3759-31.4278-18.9526-0.0463
100.35340.5322-0.47360.8256-0.56940.38260.42191.33970.7698-0.6038-0.2705-0.3878-0.16160.29890.20760.33740.06810.07360.57630.06380.3403-31.1646-18.6787-12.7249
110.5613-0.4267-0.48760.2290.39670.3820.18040.34210.6808-0.2207-0.2601-0.6505-0.3190.2647-0.00230.4043-0.01020.07320.52140.02040.423-27.831-15.6188-7.9524
120.6164-0.4052-0.68630.25380.28440.67290.0001-0.15630.4593-0.15530.10670.1003-0.26810.07200.2992-0.01820.00540.31920.00520.394-40.3882-14.5869-5.3252
130.2970.3485-0.2310.4238-0.18690.1325-0.03520.0280.4965-0.74890.3817-0.49580.04870.09430.02130.29830.01160.07690.4428-0.08460.3371-30.9799-24.4251-10.4195
140.38680.6403-0.43361.3955-0.37760.3580.1582-0.31660.5151-0.1066-0.05310.0429-0.12680.2076-0.00070.2970.00020.00540.3738-0.08310.2992-37.9854-21.38952.2183
150.14150.1743-0.11050.3018-0.28440.20180.26110.3178-0.599-0.2605-0.1567-0.17890.6097-0.0208-0.00030.38720.0240.02610.3929-0.00380.5689-58.426-20.7693-0.4763
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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