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- PDB-6ydv: Crystal Structure of the Jmjc Domain of Human JMJD1B in complex w... -

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Basic information

Entry
Database: PDB / ID: 6ydv
TitleCrystal Structure of the Jmjc Domain of Human JMJD1B in complex with FM001511a from the DSPL fragment library
ComponentsJMJD1B protein
KeywordsOXIDOREDUCTASE / Fragment / Complex / KDM3B / Xchem / Structural Genomics
Function / homology
Function and homology information


demethylation / [histone H3]-dimethyl-L-lysine9 demethylase / histone H3K9 demethylase activity / histone deacetylase complex / transcription coregulator activity / chromatin DNA binding / regulation of transcription by RNA polymerase II / chromatin / metal ion binding
Similarity search - Function
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
: / Chem-ONQ / Lysine-specific demethylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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: Crystal Structure of the Jmjc Domain of Human JMJD1B in complex with FM001511a from 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 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: JMJD1B protein
BBB: JMJD1B protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,64610
Polymers86,1512
Non-polymers4958
Water11,331629
1
AAA: JMJD1B protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4807
Polymers43,0761
Non-polymers4056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: JMJD1B protein
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)57.600, 93.790, 92.610
Angle α, β, γ (deg.)90.000, 107.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein JMJD1B protein


Mass: 43075.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JMJD1B / Production host: Escherichia coli (E. coli) / References: UniProt: A4FUT8
#2: Chemical ChemComp-ONQ / ~{N}-(2-azanyl-2-oxidanylidene-ethyl)-4-methoxy-benzamide


Mass: 208.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O3 / 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.: 629 / 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: 2.77 Å3/Da / Density % sol: 55.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M bis-tris pH 5.5, 24% PEG3350, 0.4M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.07→54.934 Å / Num. obs: 56778 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 32.041 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.069 / Rrim(I) all: 0.13 / Net I/σ(I): 10.2
Reflection shellResolution: 2.07→9.26 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.961 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4190 / CC1/2: 0.556 / Rpim(I) all: 0.713 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RBJ

6rbj


Resolution: 2.07→54.934 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.146 / SU B: 13.587 / SU ML: 0.149 / Average fsc free: 0.8542 / Average fsc work: 0.8698 / Cross valid method: FREE R-VALUE / ESU R Free: 0.152
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2137 2774 4.888 %
Rwork0.1696 53982 -
all0.172 --
obs-56756 99.122 %
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: 40.58 Å2
Baniso -1Baniso -2Baniso -3
1-3.129 Å20 Å20.238 Å2
2---3.372 Å20 Å2
3---0.077 Å2
Refinement stepCycle: LAST / Resolution: 2.07→54.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5506 0 22 629 6157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0135668
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175098
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.6437691
X-RAY DIFFRACTIONr_angle_other_deg1.2331.58511848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2055681
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.6722.615325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61615949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3861537
X-RAY DIFFRACTIONr_chiral_restr0.0590.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026417
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021202
X-RAY DIFFRACTIONr_nbd_refined0.1830.21005
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.24386
X-RAY DIFFRACTIONr_nbtor_refined0.1540.22569
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22184
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2404
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1290.215
X-RAY DIFFRACTIONr_nbd_other0.1920.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4820.217
X-RAY DIFFRACTIONr_mcbond_it2.1474.0782734
X-RAY DIFFRACTIONr_mcbond_other2.1374.0762733
X-RAY DIFFRACTIONr_mcangle_it2.4656.1013411
X-RAY DIFFRACTIONr_mcangle_other2.4656.1033412
X-RAY DIFFRACTIONr_scbond_it2.2814.5112934
X-RAY DIFFRACTIONr_scbond_other2.284.5082932
X-RAY DIFFRACTIONr_scangle_it2.5726.5854280
X-RAY DIFFRACTIONr_scangle_other2.5716.5854280
X-RAY DIFFRACTIONr_lrange_it3.48448.3336277
X-RAY DIFFRACTIONr_lrange_other3.16947.6436127
X-RAY DIFFRACTIONr_rigid_bond_restr0.688310766
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
2.07-2.1240.3431930.31339930.31442230.6250.65499.12380.302
2.124-2.1820.3531990.29838550.30140920.6060.63799.07140.285
2.182-2.2450.2932100.28137040.28239870.740.7498.1690.265
2.245-2.3140.3051660.24537030.24838910.7940.81899.43460.222
2.314-2.390.2471780.21735920.21937790.8370.86199.76180.198
2.39-2.4730.2572090.21233680.21535930.8750.87999.55470.191
2.473-2.5670.2671720.20133160.20535110.8770.89599.34490.177
2.567-2.6710.221970.17631860.17834060.9160.92899.32470.155
2.671-2.790.2281700.16530320.16832270.9180.93799.22530.14
2.79-2.9250.2431570.16329250.16731260.9150.93798.59240.14
2.925-3.0830.2061110.15927900.1629410.9260.9498.63990.137
3.083-3.270.2591190.15926100.16427960.9190.94197.60370.14
3.27-3.4940.1991300.14225010.14526410.9450.95999.62140.127
3.494-3.7730.1951090.1423570.14224680.9460.96699.9190.13
3.773-4.1310.1561090.12221390.12422530.9720.97599.77810.114
4.131-4.6160.139990.10919470.11120500.9780.98299.80490.104
4.616-5.3230.171690.12917340.1318150.970.97799.33880.122
5.323-6.5050.179920.15814120.1615510.9650.96696.96970.148
6.505-9.1350.168510.16711500.16712030.9530.95899.83370.163
9.135-54.9340.17340.1736670.1737030.9660.96699.71550.177

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