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- PDB-5uqd: DPY-21 in complex with Fe(II) and alpha-Ketoglutarate -

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Basic information

Entry
Database: PDB / ID: 5uqd
TitleDPY-21 in complex with Fe(II) and alpha-Ketoglutarate
ComponentsDumPY: shorter than wild-type
KeywordsOXIDOREDUCTASE / JmjC / H4K20me2 demethylase
Function / homologyRSBN1/Dpy-21 / histone H4K20 demethylase activity / 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 / X chromosome / metal ion binding / nucleus / 2-OXOGLUTARIC ACID / : / Lysine-specific demethylase 9
Function and homology information
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.798 Å
AuthorsBrejc, K. / Bian, Q. / Uzawa, S. / Wheeler, B.S. / Anderson, E.C. / King, D.S. / Kranzusch, P.J. / Preston, C.G. / Meyer, B.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM030702 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100647 United States
CitationJournal: Cell / Year: 2017
Title: Dynamic Control of X Chromosome Conformation and Repression by a Histone H4K20 Demethylase.
Authors: Brejc, K. / Bian, Q. / Uzawa, S. / Wheeler, B.S. / Anderson, E.C. / King, D.S. / Kranzusch, P.J. / Preston, C.G. / Meyer, B.J.
History
DepositionFeb 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Feb 26, 2020Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rpim_I_all
Revision 1.6Mar 17, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.7Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: DumPY: shorter than wild-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0745
Polymers50,6321
Non-polymers4424
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.625, 97.883, 98.838
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1945-

HOH

DetailsMonomer as determined by size exclusion chromatography

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Components

#1: Protein DumPY: shorter than wild-type


Mass: 50631.773 Da / Num. of mol.: 1 / Fragment: residues 1210-1617
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: dpy-21, CELE_Y59A8B.1, Y59A8B.1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: Q9GRZ3
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Crystals were grown in hanging drops containing 200 nl DPY-21 (5 mg/ml) and 200 nl well solution containing 100 mM DL-malic acid (pH 5.6) and 25% (w/v) PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.798→43.86 Å / Num. obs: 39587 / % possible obs: 99.5 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rpim(I) all: 0.036 / Net I/σ(I): 14

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.798→43.859 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1928 1978 5 %Random selection
Rwork0.1634 ---
obs0.1649 39536 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.798→43.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2623 0 27 254 2904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152799
X-RAY DIFFRACTIONf_angle_d1.2053783
X-RAY DIFFRACTIONf_dihedral_angle_d14.1751703
X-RAY DIFFRACTIONf_chiral_restr0.086399
X-RAY DIFFRACTIONf_plane_restr0.009497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7983-1.84330.3131360.25792577X-RAY DIFFRACTION96
1.8433-1.89320.23581380.21332624X-RAY DIFFRACTION99
1.8932-1.94890.22251400.19952635X-RAY DIFFRACTION99
1.9489-2.01180.2021390.16762663X-RAY DIFFRACTION99
2.0118-2.08370.20921390.15972643X-RAY DIFFRACTION99
2.0837-2.16710.20371420.15422681X-RAY DIFFRACTION100
2.1671-2.26570.21481400.14882662X-RAY DIFFRACTION100
2.2657-2.38520.18251400.1562668X-RAY DIFFRACTION100
2.3852-2.53460.21091430.15752697X-RAY DIFFRACTION100
2.5346-2.73030.17351410.15982690X-RAY DIFFRACTION100
2.7303-3.0050.20421420.16782702X-RAY DIFFRACTION100
3.005-3.43960.18521430.16072717X-RAY DIFFRACTION100
3.4396-4.3330.17481440.1442752X-RAY DIFFRACTION100
4.333-43.87210.17461510.1692847X-RAY DIFFRACTION100
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)
14.1664-0.3543-0.10044.1336-1.10022.4733-0.21780.156-0.5031-0.05780.04630.05850.72660.08330.15730.31570.09030.05320.1686-0.04620.23558.72338.641317.9882
20.5275-0.1744-0.08341.06640.72691.909-0.0592-0.0507-0.15590.16950.0423-0.02150.56080.32570.01770.22840.05980.02250.16220.01760.186558.528716.273631.8055
35.0865-1.39031.18093.8349-0.20580.7319-0.4065-0.50050.7293-0.1390.0178-0.0849-0.3393-0.17910.2610.26270.0407-0.07930.1541-0.04950.21453.852841.162750.0167
42.0665-0.4880.47042.14150.7612.3582-0.1429-0.22520.13520.11480.239-0.41590.15580.5382-0.08060.18580.0421-0.01240.2711-0.00120.145262.312927.861542.794
52.12860.2455-0.00151.86480.24921.7844-0.0492-0.09480.11960.05280.0382-0.0566-0.11210.0957-0.00030.18360.0085-0.02750.1676-0.00990.115652.689732.050735.5572
61.4334-0.08680.06860.8129-0.13342.8466-0.04960.05050.2116-0.02050.0405-0.128-0.25070.32450.01130.137-0.03180.00420.1406-0.01210.167258.002232.533924.2979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1208 through 1237 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1238 through 1310 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1311 through 1342 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1343 through 1412 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1413 through 1523 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1524 through 1610 )

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