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- PDB-5rb5: PanDDA analysis group deposition -- Crystal Structure of JMJD1B i... -

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Basic information

Entry
Database: PDB / ID: 5rb5
TitlePanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM010010a
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
: / ~{N}-[2-(4-fluorophenyl)ethyl]methanesulfonamide / Lysine-specific demethylase 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.51 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)87,09012
Polymers86,1512
Non-polymers93910
Water12,574698
1
A: Lysine-specific demethylase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7078
Polymers43,0761
Non-polymers6317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine-specific demethylase 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3834
Polymers43,0761
Non-polymers3083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.930, 93.600, 93.810
Angle α, β, γ (deg.)90.000, 107.800, 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-S9S / ~{N}-[2-(4-fluorophenyl)ethyl]methanesulfonamide


Mass: 217.260 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H12FNO2S / 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.: 698 / 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: 56.24 % / 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: 1.51→55.05 Å / Num. obs: 147574 / % possible obs: 99 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.027 / Rrim(I) all: 0.051 / Net I/σ(I): 14.3 / Num. measured all: 505592 / 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
1.51-1.553.51.08438192108970.5430.6771.2831.299.3
6.75-55.053.60.018615217050.9970.0120.02262.898.7

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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: 1.51→55.11 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.908 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 7406 5 %RANDOM
Rwork0.1851 ---
obs0.1862 140128 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.54 Å2 / Biso mean: 27.578 Å2 / Biso min: 12.54 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20 Å2-0.34 Å2
2---1.26 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.51→55.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5514 0 49 698 6261
Biso mean--31.05 38.7 -
Num. residues----684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0147177
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175856
X-RAY DIFFRACTIONr_angle_refined_deg1.7991.6568971
X-RAY DIFFRACTIONr_angle_other_deg1.3631.60213637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3325825
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.27222.283381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.997151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8251549
X-RAY DIFFRACTIONr_chiral_restr0.0890.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027880
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021467
X-RAY DIFFRACTIONr_mcbond_it2.712.6693498
X-RAY DIFFRACTIONr_mcbond_other2.7242.6563463
X-RAY DIFFRACTIONr_mcangle_it4.2523.9824059
LS refinement shellResolution: 1.51→1.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 563 -
Rwork0.321 10317 -
all-10880 -
obs--99.15 %

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