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- PDB-4fwj: Native structure of LSD2/AOF1/KDM1b in spacegroup of I222 at 2.9A -

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Basic information

Entry
Database: PDB / ID: 4fwj
TitleNative structure of LSD2/AOF1/KDM1b in spacegroup of I222 at 2.9A
ComponentsLysine-specific histone demethylase 1B
KeywordsOXIDOREDUCTASE / lsd2 / fad / histone demethylase / C4H2C2 / CW / epigenetic
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 / : / PHOSPHATE ION / Lysine-specific histone demethylase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhang, Q. / Chen, Z.
CitationJournal: Cell Res. / Year: 2013
Title: Structure-function analysis reveals a novel mechanism for regulation of histone demethylase LSD2/AOF1/KDM1b
Authors: Zhang, Q. / Qi, S. / Xu, M. / Yu, L. / Tao, Y. / Deng, Z. / Wu, W. / Li, J. / Chen, Z. / Wong, J.
History
DepositionJul 1, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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)180,78012
Polymers178,6822
Non-polymers2,09810
Water8,359464
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A: Lysine-specific histone demethylase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3626
Polymers89,3411
Non-polymers1,0215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysine-specific histone demethylase 1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4186
Polymers89,3411
Non-polymers1,0775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-13 kcal/mol
Surface area63380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.322, 170.933, 202.566
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 89340.977 Da / Num. of mol.: 2 / Fragment: UNP residues 30-822
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LSD2 / Plasmid: pet-28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NB78, Oxidoreductases

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Non-polymers , 5 types, 474 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: 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
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 3.5 Å3/Da / Density % sol: 64.82 %

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 55698 / Num. obs: 55566 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.113 / Rsym value: 0.093 / Net I/σ(I): 15.7
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2759 / Rsym value: 0.346 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
REFMAC5.6.0116refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HKO

2hko


Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / SU B: 22.144 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 3 / σ(I): 3 / ESU R: 0.911 / ESU R Free: 0.314 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22233 2818 5.1 %RANDOM
Rwork0.18628 ---
all0.18813 55698 --
obs0.18813 52723 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.586 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2---2.96 Å20 Å2
3---3.67 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11480 0 118 464 12062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211907
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.96416189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04351491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80723.911496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.748151881
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8541558
X-RAY DIFFRACTIONr_chiral_restr0.0880.21768
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219048
LS refinement shellResolution: 2.899→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 203 -
Rwork0.303 3559 -
obs-2818 97.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2790.5143-0.64462.89250.05852.0647-0.17980.21750.0559-0.0430.1802-0.6613-0.10060.4135-0.00040.0396-0.0456-0.05450.1495-0.04240.3236-11.115837.806734.0202
21.5794-0.818-0.50573.93261.23051.7985-0.10060.0784-0.07250.06480.1075-0.28430.04050.1402-0.00690.0314-0.0163-0.01920.0551-0.04050.1147-20.625131.203738.6926
39.65844.31511.66711.93725.216714.1031-0.02260.9869-0.5834-0.08310.4997-0.2326-0.28191.156-0.4771.1702-0.01110.6741.1578-0.192.562-13.358311.003837.0055
41.17571.2924-0.31464.4652-0.44010.1805-0.0163-0.0070.0238-0.02660.0863-0.18970.0617-0.0251-0.06990.05380.006-0.05720.0431-0.0190.0969-31.079318.976236.4394
53.34690.3482-1.4368.85184.75983.36360.0949-0.69070.98331.14420.4783-0.16960.5080.5537-0.57320.79170.1079-0.02120.8013-0.09560.5744-45.920723.798851.9956
60.90860.33970.03311.2426-0.34770.46630.0099-0.12450.05020.15240.02850.05030.02320.0392-0.03840.1246-0.0131-0.06250.05720.00190.0642-46.70840.257547.2476
72.4105-0.98150.21092.0990.30272.29860.00360.18940.0076-0.2747-0.0870.021-0.0628-0.02080.08350.1821-0.0294-0.03240.1539-0.03260.0202-48.5087-18.603218.5036
81.0382-0.4003-0.10791.6534-0.0391.0547-0.01790.020.09560.06240.06840.2251-0.0083-0.1088-0.05040.0639-0.0227-0.02530.04750.0190.081-57.98813.654339.2947
90.6932-0.69730.72111.3545-0.38012.2775-0.0239-0.1094-0.16770.03850.0822-0.0383-0.1399-0.1874-0.05830.1150.0083-0.03590.10840.02940.1468-46.6507-23.661840.283
101.01090.1915-0.05910.42590.05850.12640.04610.02090.0588-0.063-0.04050.22050.0259-0.0345-0.00560.12540.0064-0.05560.0924-0.01030.1296-54.5405-6.727338.446
111.1701-1.6906-1.48982.47222.25064.4620.0610.0161-0.0502-0.05170.1422-0.0241.18690.9392-0.20330.65610.2948-0.03031.0496-0.23870.5905-21.122422.1518-3.0067
121.92580.20680.64942.12721.44344.6986-0.20430.07180.0793-0.20390.2193-0.3844-0.25251.3-0.0150.1581-0.08690.06820.48230.01020.108-24.408936.89040.5542
1321.5031-0.9363-5.20570.09390.17691.30871.70882.22261.4868-0.0084-0.8861-0.1016-0.6662-0.2677-0.82271.6694-0.23750.00531.80650.30380.8065-34.06445.003-18.9263
141.2998-0.52611.1351.28691.58216.90430.0049-0.0380.00280.066-0.0192-0.11990.3440.35020.01430.1331-0.03650.06370.17610.00580.0779-33.102834.27075.9568
1512.99616.4678-19.81853.3217-9.97730.34961.85121.49420.14911.3697-0.8086-0.1671-4.3392-1.6801-1.04260.77410.48260.46083.6852-0.13552.4812-29.304754.463415.7116
161.4235-1.1252-0.72832.05991.45051.0397-0.03730.08180.0976-0.21630.0445-0.033-0.19160.0652-0.00720.1342-0.0471-0.06050.08860.0040.0434-42.832941.151615.4995
174.09535.45439.26797.312.399821.0653-0.2889-0.23650.3496-0.2943-0.52960.5034-0.4668-0.7950.81850.6308-0.01610.05860.9184-0.00060.6763-61.558539.56057.7603
181.38180.63260.35191.3670.3461.0217-0.0435-0.01440.2391-0.0676-0.08280.1969-0.0487-0.11220.12620.04630.0409-0.07370.0493-0.05360.154-61.205251.967538.0696
191.3473-0.4711.00842.96161.44593.554-0.2971-0.24580.6566-0.2125-0.09890.3014-0.2465-0.12940.3960.12090.0973-0.23990.0831-0.18530.5547-61.546172.111142.4462
201.30650.98970.78051.10470.14361.0342-0.0653-0.10210.3294-0.0531-0.03910.3363-0.0381-0.12340.10450.02990.0285-0.07940.059-0.06690.2521-65.555654.357437.3566
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A48 - 170
2X-RAY DIFFRACTION2A171 - 233
3X-RAY DIFFRACTION3A234 - 264
4X-RAY DIFFRACTION4A265 - 367
5X-RAY DIFFRACTION5A368 - 384
6X-RAY DIFFRACTION6A385 - 462
7X-RAY DIFFRACTION7A463 - 547
8X-RAY DIFFRACTION8A548 - 662
9X-RAY DIFFRACTION9A663 - 723
10X-RAY DIFFRACTION10A724 - 822
11X-RAY DIFFRACTION11B51 - 89
12X-RAY DIFFRACTION12B90 - 170
13X-RAY DIFFRACTION13B171 - 183
14X-RAY DIFFRACTION14B184 - 233
15X-RAY DIFFRACTION15B234 - 265
16X-RAY DIFFRACTION16B266 - 367
17X-RAY DIFFRACTION17B368 - 383
18X-RAY DIFFRACTION18B384 - 661
19X-RAY DIFFRACTION19B662 - 723
20X-RAY DIFFRACTION20B724 - 822

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