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- PDB-4gu1: Crystal structure of LSD2 -

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Basic information

Entry
Database: PDB / ID: 4gu1
TitleCrystal structure of LSD2
ComponentsLysine-specific histone demethylase 1B
KeywordsOXIDOREDUCTASE / histone demethylase
Function / homology
Function and homology information


epigenetic programing of female pronucleus / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / genomic imprinting / histone demethylase activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling / FAD binding / HDMs demethylate histones / UCH proteinases ...epigenetic programing of female pronucleus / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / genomic imprinting / histone demethylase activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription initiation-coupled chromatin remodeling / FAD binding / HDMs demethylate histones / UCH proteinases / nucleosome / flavin adenine dinucleotide binding / histone binding / oxidoreductase activity / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / SWIRM domain / SWIRM domain / SWIRM domain profile. / Amine oxidase / Flavin containing amine oxidoreductase / Homeobox-like domain superfamily / FAD/NAD(P)-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Lysine-specific histone demethylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.939 Å
AuthorsChen, F. / Dong, Z. / Fang, J. / Yang, Y. / Li, Z. / Xu, Y. / Yang, H. / Wang, P. / Fang, R. / Shi, Y. / Xu, Y.
CitationJournal: Mol.Cell / Year: 2013
Title: LSD2/KDM1B and its cofactor NPAC/GLYR1 endow a structural and molecular model for regulation of H3K4 demethylation
Authors: Fang, R. / Chen, F. / Dong, Z. / Hu, D. / Barbera, A.J. / Clark, E.A. / Fang, J. / Yang, Y. / Mei, P. / Rutenberg, M. / Li, Z. / Zhang, Y. / Xu, Y. / Yang, H. / Wang, P. / Simon, M.D. / ...Authors: Fang, R. / Chen, F. / Dong, Z. / Hu, D. / Barbera, A.J. / Clark, E.A. / Fang, J. / Yang, Y. / Mei, P. / Rutenberg, M. / Li, Z. / Zhang, Y. / Xu, Y. / Yang, H. / Wang, P. / Simon, M.D. / Zhou, Q. / Li, J. / Marynick, M.P. / Li, X. / Lu, H. / Kaiser, U.B. / Kingston, R.E. / Xu, Y. / Shi, Y.G.
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific histone demethylase 1B
B: Lysine-specific histone demethylase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,34916
Polymers176,1982
Non-polymers2,15114
Water41423
1
A: Lysine-specific histone demethylase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1748
Polymers88,0991
Non-polymers1,0767
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine-specific histone demethylase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1748
Polymers88,0991
Non-polymers1,0767
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10080 Å2
ΔGint-97 kcal/mol
Surface area61560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.163, 89.216, 342.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lysine-specific histone demethylase 1B / LSD2 / Flavin-containing amine oxidase domain-containing protein 1 / Lysine-specific histone demethylase 2


Mass: 88098.805 Da / Num. of mol.: 2 / Fragment: UNP residues 51-822
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LSD2 / Plasmid: pFastBac1 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8NB78, Oxidoreductases

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Non-polymers , 5 types, 37 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.87 Å3/Da / Density % sol: 68.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M Sodium chloride, 0.1M Na/K phosphate, 7% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97947 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 57805 / % possible obs: 91.79 % / Biso Wilson estimate: 83.09 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V1D

2v1d


Resolution: 2.939→39.562 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7908 / SU ML: 0.41 / σ(F): 1.33 / Phase error: 26.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 2922 5.06 %
Rwork0.185 54841 -
obs0.1872 57763 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.53 Å2 / Biso mean: 83.4378 Å2 / Biso min: 46.92 Å2
Refinement stepCycle: LAST / Resolution: 2.939→39.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11830 0 118 23 11971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112236
X-RAY DIFFRACTIONf_angle_d1.34216584
X-RAY DIFFRACTIONf_chiral_restr0.0921782
X-RAY DIFFRACTIONf_plane_restr0.012114
X-RAY DIFFRACTIONf_dihedral_angle_d19.7744582
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9389-2.98710.4458870.3091743183066
2.9871-3.03860.33451150.29532604271998
3.0386-3.09380.36531310.29422624275599
3.0938-3.15330.37611220.28462627274999
3.1533-3.21760.36011440.28032626277099
3.2176-3.28750.3181160.26012634275099
3.2875-3.3640.30221490.25792582273199
3.364-3.44810.32341690.25626712840100
3.4481-3.54120.351240.23362618274299
3.5412-3.64540.2671510.21532600275199
3.6454-3.76290.21911650.20662644280999
3.7629-3.89730.22191550.1952620277599
3.8973-4.05320.24471180.17522690280899
4.0532-4.23750.20751430.16222634277799
4.2375-4.46060.21511260.15472666279299
4.4606-4.73970.18551310.142826742805100
4.7397-5.10490.16051300.134626992829100
5.1049-5.61730.21881610.146926922853100
5.6173-6.42720.19861640.161327232887100
6.4272-8.08620.20851690.165227372906100
8.0862-39.56580.18121520.17592733288595

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