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- PDB-5rar: PanDDA analysis group deposition -- Crystal Structure of JMJD1B i... -

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Basic information

Entry
Database: PDB / ID: 5rar
TitlePanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with TD000005c
ComponentsLysine-specific demethylase 3B
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / antioxidant activity / histone H3K9 demethylase activity / histone deacetylase complex / transcription coregulator activity / HDMs demethylate histones / chromatin DNA binding / chromatin / regulation of transcription by RNA polymerase II ...histone H3K9me/H3K9me2 demethylase activity / [histone H3]-dimethyl-L-lysine9 demethylase / antioxidant activity / histone H3K9 demethylase activity / histone deacetylase complex / transcription coregulator activity / HDMs demethylate histones / chromatin DNA binding / 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 / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. ...: / Lysine-specific demethylase 3B, PWWP domain / Domain of unknown function (DUF7030) / Histone demethylase JHDM2-like / Lysine-specific demethylase 3B, tudor domain / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / 2-[4-[(3~{S})-pyrazolidin-3-yl]phenoxy]pyrimidine / Lysine-specific demethylase 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.47 Å
AuthorsSnee, M. / Nowak, R. / Johansson, C. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Oppermann, U.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition of Human JMJD1B screened against the DSPL Fragment Library
Authors: Snee, M. / Nowak, R. / Johansson, C. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Oppermann, U.
History
DepositionMar 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 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

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Assembly

Deposited unit
A: Lysine-specific demethylase 3B
B: Lysine-specific demethylase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,92311
Polymers86,1512
Non-polymers7729
Water12,701705
1
A: Lysine-specific demethylase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7578
Polymers43,0761
Non-polymers6817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine-specific demethylase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1663
Polymers43,0761
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.750, 93.410, 94.215
Angle α, β, γ (deg.)90.000, 107.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lysine-specific demethylase 3B / JmjC domain-containing histone demethylation protein 2B / Jumonji domain-containing protein 1B / ...JmjC domain-containing histone demethylation protein 2B / Jumonji domain-containing protein 1B / Nuclear protein 5qNCA


Mass: 43075.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM3B, C5orf7, JHDM2B, JMJD1B, KIAA1082 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7LBC6, 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: Chemical ChemComp-S9D / 2-[4-[(3~{S})-pyrazolidin-3-yl]phenoxy]pyrimidine


Mass: 242.276 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H14N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 705 / 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: 2.81 Å3/Da / Density % sol: 56.2 % / Mosaicity: 0 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M bis-tris pH 5.5 21% PEG3350 0.3M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.47→47.38 Å / Num. obs: 157969 / % possible obs: 98 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.023 / Rrim(I) all: 0.042 / Net I/σ(I): 17.2 / Num. measured all: 540576 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.47-1.513.21.00336278112940.520.6531.2021.395.5
6.57-47.383.60.018675518520.9990.0110.02173.298.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimless0.5.17data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6RBJ

6rbj


Resolution: 1.47→47.42 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.592 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 7849 5 %RANDOM
Rwork0.1829 ---
obs0.184 150105 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.23 Å2 / Biso mean: 27.374 Å2 / Biso min: 8.96 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å2-0 Å2-0.43 Å2
2---0.96 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.47→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5506 0 43 705 6254
Biso mean--35.47 38.35 -
Num. residues----684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0147572
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176132
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.6589273
X-RAY DIFFRACTIONr_angle_other_deg1.381.59914269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5125840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.05522.094406
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.499151165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6281555
X-RAY DIFFRACTIONr_chiral_restr0.10.2833
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027836
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021489
X-RAY DIFFRACTIONr_mcbond_it2.5212.7373657
X-RAY DIFFRACTIONr_mcbond_other2.5352.7183614
X-RAY DIFFRACTIONr_mcangle_it4.0323.9894146
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 513 -
Rwork0.322 10768 -
all-11281 -
obs--95.13 %

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