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- PDB-9gdk: Jumonji domain-containing protein 1C with crystallization epitope... -

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Basic information

Entry
Database: PDB / ID: 9gdk
TitleJumonji domain-containing protein 1C with crystallization epitope mutations L2440Y:G2444H
ComponentsProbable JmjC domain-containing histone demethylation protein 2C
KeywordsTRANSCRIPTION / Crystal Epitopes / Bromodomain
Function / homology
Function and homology information


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 / nuclear thyroid hormone receptor binding / dioxygenase activity / histone H3K9 demethylase activity / histone deacetylase complex / transcription coregulator activity / chromatin DNA binding / blood coagulation / Factors involved in megakaryocyte development and platelet production / regulation of DNA-templated transcription ...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 / nuclear thyroid hormone receptor binding / dioxygenase activity / histone H3K9 demethylase activity / histone deacetylase complex / transcription coregulator activity / chromatin DNA binding / blood coagulation / Factors involved in megakaryocyte development and platelet production / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding
Similarity search - Function
: / Lysine-specific demethylase 3B, PWWP domain / Domain of unknown function (DUF7030) / Histone demethylase JHDM2-like / Lysine-specific demethylase 3B, tudor domain / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile.
Similarity search - Domain/homology
Probable JmjC domain-containing histone demethylation protein 2C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsFairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. ...Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Koekemoer, L. / Damerell, D. / Krojer, T. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A fast, parallel method for efficiently exploring crystallization behaviour of large numbers of protein variants
Authors: Fairhead, M. / Strain-Damerell, C. / Ye, M. / Mackinnon, S.R. / Pinkas, D. / MacLean, E.M. / Damerell, D. / Krojer, T. / Yue, W. / Burgess-Brown, N. / Marsden, B. / von Delft, F.
History
DepositionAug 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable JmjC domain-containing histone demethylation protein 2C
B: Probable JmjC domain-containing histone demethylation protein 2C


Theoretical massNumber of molelcules
Total (without water)79,9032
Polymers79,9032
Non-polymers00
Water10,665592
1
A: Probable JmjC domain-containing histone demethylation protein 2C


Theoretical massNumber of molelcules
Total (without water)39,9521
Polymers39,9521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable JmjC domain-containing histone demethylation protein 2C


Theoretical massNumber of molelcules
Total (without water)39,9521
Polymers39,9521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.2, 98.25, 87.4
Angle α, β, γ (deg.)90, 92.04, 90
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 2156 - 2500 / Label seq-ID: 2 - 346

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Probable JmjC domain-containing histone demethylation protein 2C / Jumonji domain-containing protein 1C / Thyroid receptor-interacting protein 8 / TR-interacting ...Jumonji domain-containing protein 1C / Thyroid receptor-interacting protein 8 / TR-interacting protein 8 / TRIP-8


Mass: 39951.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD1C, JHDM2C, KIAA1380, TRIP8 / Production host: Escherichia coli (E. coli)
References: UniProt: Q15652, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O
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: 2.43 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: LFS well F04 20% PEG3350 10% ethylene glycol 0.1M bis-tris-propane pH 6.5 0.2M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.78→31.37 Å / Num. obs: 71577 / % possible obs: 98.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 12
Reflection shellResolution: 1.78→1.83 Å / Rmerge(I) obs: 0.936 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 18899 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.77)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→31.369 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.456 / SU ML: 0.106 / Cross valid method: FREE R-VALUE / ESU R: 0.14 / ESU R Free: 0.13 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2422 3511 4.907 %
Rwork0.2093 68041 -
all0.211 --
obs-71552 97.995 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.142 Å2
Baniso -1Baniso -2Baniso -3
1--1.142 Å2-0 Å2-0.721 Å2
2--1.198 Å2-0 Å2
3----0.005 Å2
Refinement stepCycle: LAST / Resolution: 1.78→31.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5267 0 0 607 5874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125471
X-RAY DIFFRACTIONr_angle_refined_deg1.8591.8057455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.45690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.147519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07110874
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.60110240
X-RAY DIFFRACTIONr_chiral_restr0.140.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024263
X-RAY DIFFRACTIONr_nbd_refined0.4120.23252
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23675
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.280.2571
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4910.2204
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3570.218
X-RAY DIFFRACTIONr_mcbond_it3.2993.112751
X-RAY DIFFRACTIONr_mcangle_it4.9225.5643444
X-RAY DIFFRACTIONr_scbond_it4.3723.3372720
X-RAY DIFFRACTIONr_scangle_it6.7115.9994011
X-RAY DIFFRACTIONr_lrange_it27.45269.6629522
X-RAY DIFFRACTIONr_ncsr_local_group_10.1150.0510269
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.114680.05008
12BX-RAY DIFFRACTIONLocal ncs0.114680.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.78-1.8260.322890.30450520.30553740.9320.9499.38590.288
1.826-1.8760.3272650.28849410.2952360.9340.94599.4270.265
1.876-1.930.32120.24648060.24850650.9460.95999.07210.223
1.93-1.9890.2692290.23646700.23849560.9480.96398.84990.21
1.989-2.0540.272620.22745120.2348180.9530.96599.08680.201
2.054-2.1260.2562170.21543670.21746310.9550.9798.98510.193
2.126-2.2060.252030.21441760.21544400.9570.9798.62610.192
2.206-2.2960.2792150.2239660.22443360.9510.96996.42530.197
2.296-2.3970.261830.20836700.21141280.9540.97293.33820.186
2.397-2.5130.241790.20137960.20339860.9610.97499.7240.18
2.513-2.6480.261950.20435380.20737420.9560.97399.75950.184
2.648-2.8080.2111640.19933680.235480.9660.97599.5490.181
2.808-30.2241830.19331620.19433840.9680.97698.84750.18
3-3.2380.2591570.229200.20331260.9560.97498.43250.189
3.238-3.5430.261180.19226340.19528500.9640.97896.56140.187
3.543-3.9550.2071260.18823960.18926220.9730.97996.18610.189
3.955-4.5550.1991050.17520280.17723350.9790.98191.3490.181
4.555-5.5490.19980.17717720.17819640.980.98195.21390.185
5.549-7.7280.26710.23514200.23715470.9680.97196.38010.238
7.728-31.3690.236400.278470.2699130.9740.9697.15220.295

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