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- PDB-4gut: Crystal structure of LSD2-NPAC -

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Basic information

Entry
Database: PDB / ID: 4gut
TitleCrystal structure of LSD2-NPAC
Components
  • Lysine-specific histone demethylase 1B
  • Putative oxidoreductase GLYR1
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 / chromatin-protein adaptor activity / transcription elongation-coupled chromatin remodeling / histone demethylase activity / nucleosome binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / FAD binding ...epigenetic programing of female pronucleus / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / genomic imprinting / chromatin-protein adaptor activity / transcription elongation-coupled chromatin remodeling / histone demethylase activity / nucleosome binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / FAD binding / transcription initiation-coupled chromatin remodeling / HDMs demethylate histones / NAD binding / UCH proteinases / nucleosome / NADP binding / histone binding / oxidoreductase activity / chromatin binding / chromatin / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
NP60, PWWP domain / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / : / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / SWIRM domain ...NP60, PWWP domain / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / Zinc finger, CW-type / CW-type Zinc Finger / Zinc finger CW-type profile. / : / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / SWIRM domain / SWIRM domain / SWIRM domain profile. / : / 6-phosphogluconate dehydrogenase, domain 2 / Amine oxidase / Flavin containing amine oxidoreductase / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Homeobox-like domain superfamily / FAD/NAD(P)-binding domain superfamily / NAD(P)-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL / Cytokine-like nuclear factor N-PAC / Lysine-specific histone demethylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.998 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Putative oxidoreductase GLYR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8969
Polymers100,5802
Non-polymers1,3167
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-13 kcal/mol
Surface area31560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.000, 89.762, 86.694
Angle α, β, γ (deg.)90.00, 104.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 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: 87051.547 Da / Num. of mol.: 1 / 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
#2: Protein Putative oxidoreductase GLYR1 / NPAC / 3-hydroxyisobutyrate dehydrogenase-like protein / Cytokine-like nuclear factor N-PAC / ...NPAC / 3-hydroxyisobutyrate dehydrogenase-like protein / Cytokine-like nuclear factor N-PAC / Glyoxylate reductase 1 homolog / Nuclear protein NP60 / Nuclear protein of 60 kDa


Mass: 13528.271 Da / Num. of mol.: 1 / Fragment: UNP residues 152-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLYR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q49A26, Oxidoreductases

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Non-polymers , 5 types, 353 molecules

#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.32 Å3/Da / Density % sol: 46.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.998→50 Å / Num. all: 59253 / Num. obs: 56169 / % possible obs: 90.19 % / Biso Wilson estimate: 26.83 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: 4GU1

4gu1


Resolution: 1.998→35.917 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8474 / SU ML: 0.21 / σ(F): 0.08 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 2835 5.05 %
Rwork0.196 --
obs0.1966 56166 90.19 %
all-59253 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.899 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 99.62 Å2 / Biso mean: 39.159 Å2 / Biso min: 14.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.9863 Å2-0 Å213.3841 Å2
2---5.0071 Å2-0 Å2
3---4.0208 Å2
Refinement stepCycle: LAST / Resolution: 1.998→35.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5961 0 78 346 6385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116193
X-RAY DIFFRACTIONf_angle_d1.1478391
X-RAY DIFFRACTIONf_chiral_restr0.081900
X-RAY DIFFRACTIONf_plane_restr0.0091068
X-RAY DIFFRACTIONf_dihedral_angle_d17.3572314
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9976-2.0320.2895820.25551844192662
2.032-2.06890.2641180.24472061217969
2.0689-2.10870.25151000.24052126222673
2.1087-2.15180.25571330.24472273240677
2.1518-2.19860.24671200.22372457257784
2.1986-2.24970.26061350.23062554268987
2.2497-2.30590.28221560.23252626278289
2.3059-2.36830.20831400.22222741288193
2.3683-2.4380.25721550.22392736289193
2.438-2.51660.21711500.21412759290994
2.5166-2.60650.21111430.21292796293995
2.6065-2.71090.22421550.21892878303397
2.7109-2.83420.21931830.20872819300297
2.8342-2.98360.21491410.21672905304698
2.9836-3.17040.20941570.20582879303698
3.1704-3.4150.23441710.19982917308899
3.415-3.75830.17121240.183930003124100
3.7583-4.30140.1521660.16529463112100
4.3014-5.41630.1741600.155429713131100
5.4163-35.92290.20471460.172830433189100

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