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- PDB-4o64: Zinc fingers of KDM2B -

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Basic information

Entry
Database: PDB / ID: 4o64
TitleZinc fingers of KDM2B
ComponentsLysine-specific demethylase 2B
KeywordsMETAL BINDING PROTEIN / CXXC zinc finger / ring zinc finger / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


fourth ventricle development / initiation of neural tube closure / midbrain-hindbrain boundary morphogenesis / third ventricle development / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / embryonic camera-type eye morphogenesis / lateral ventricle development / negative regulation of neural precursor cell proliferation / hindbrain development ...fourth ventricle development / initiation of neural tube closure / midbrain-hindbrain boundary morphogenesis / third ventricle development / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / embryonic camera-type eye morphogenesis / lateral ventricle development / negative regulation of neural precursor cell proliferation / hindbrain development / PcG protein complex / unmethylated CpG binding / histone H3K36 demethylase activity / midbrain development / positive regulation of stem cell population maintenance / histone demethylase activity / forebrain development / transcription coregulator activity / HDMs demethylate histones / chromosome / positive regulation of cell growth / spermatogenesis / negative regulation of neuron apoptotic process / rRNA binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
PHD-finger / Jumonji, helical domain / Jumonji helical domain / : / Cupin-like domain 8 / Cupin-like domain / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / CXXC zinc finger domain ...PHD-finger / Jumonji, helical domain / Jumonji helical domain / : / Cupin-like domain 8 / Cupin-like domain / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / F-box domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Leucine-rich repeat domain superfamily / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Lysine-specific demethylase 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.13 Å
AuthorsLiu, K. / Xu, C. / Tempel, W. / Walker, J.R. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2018
Title: DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants.
Authors: Xu, C. / Liu, K. / Lei, M. / Yang, A. / Li, Y. / Hughes, T.R. / Min, J.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Data collection
Revision 1.2Oct 29, 2014Group: Structure summary
Revision 1.3Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _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_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
Revision 1.5Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysine-specific demethylase 2B
B: Lysine-specific demethylase 2B
C: Lysine-specific demethylase 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,83729
Polymers40,0523
Non-polymers78526
Water2,504139
1
A: Lysine-specific demethylase 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,61211
Polymers13,3511
Non-polymers26210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysine-specific demethylase 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6129
Polymers13,3511
Non-polymers2628
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lysine-specific demethylase 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6129
Polymers13,3511
Non-polymers2628
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.322, 107.322, 34.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Lysine-specific demethylase 2B / CXXC-type zinc finger protein 2 / F-box and leucine-rich repeat protein 10 / F-box protein FBL10 / ...CXXC-type zinc finger protein 2 / F-box and leucine-rich repeat protein 10 / F-box protein FBL10 / F-box/LRR-repeat protein 10 / JmjC domain-containing histone demethylation protein 1B / Jumonji domain-containing EMSY-interactor methyltransferase motif protein / Protein JEMMA / Protein-containing CXXC domain 2 / [Histone-H3]-lysine-36 demethylase 1B


Mass: 13350.738 Da / Num. of mol.: 3 / Fragment: UNP Residues 607-723
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM2B, CXXC2, FBL10, FBXL10, JHDM1B, PCCX2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: Q8NHM5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 14 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.8 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 291 K / Method: sitting drop / pH: 8.5
Details: 25% PEG 8000, 0.2 M sodium chloride, 0.1 M tris, pH 8.5, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.28315 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28315 Å / Relative weight: 1
ReflectionResolution: 2.13→46.47 Å / Num. obs: 24576 / % possible obs: 100 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 12.5
Reflection shell

Diffraction-ID: 1 / Redundancy: 5.7 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.13-2.191.0811.7112821980100
9.04-46.470.01148.3187432899.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
Aimless0.1.29data scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.13→40 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.1985 / WRfactor Rwork: 0.1686 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8204 / SU B: 10.97 / SU ML: 0.138 / SU R Cruickshank DPI: 0.1929 / SU Rfree: 0.1622 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: arp/warp was used for automated model building. coot was used for interactive model building. Model geometry was assessed on the molprobity server.
RfactorNum. reflection% reflectionSelection details
Rfree0.2198 779 3.2 %THIN SHELLS (SFTOOLS)
Rwork0.1905 ---
obs0.1914 24564 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.26 Å2 / Biso mean: 37.3248 Å2 / Biso min: 14.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.24 Å2-0 Å2
2---0.49 Å2-0 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.13→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2551 0 26 139 2716
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192724
X-RAY DIFFRACTIONr_bond_other_d0.0020.022555
X-RAY DIFFRACTIONr_angle_refined_deg1.3881.9893661
X-RAY DIFFRACTIONr_angle_other_deg0.9273.0155872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6935367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.66624.571105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65715492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9411518
X-RAY DIFFRACTIONr_chiral_restr0.0740.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213065
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02555
X-RAY DIFFRACTIONr_mcbond_it1.6192.2641409
X-RAY DIFFRACTIONr_mcbond_other1.6192.2641408
X-RAY DIFFRACTIONr_mcangle_it2.6353.3861761
LS refinement shellResolution: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.278 1774 -
obs--100 %
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)
18.4426-2.1131-2.18860.83820.38541.7813-0.1111-0.0802-0.0917-0.05690.0538-0.0060.12660.04230.05730.0314-0.0036-0.00740.0712-0.00050.095289.233151.88523.4446
23.4318-0.41570.24165.99260.8818.24480.15660.0509-0.40430.20370.0373-0.21320.25630.0778-0.19390.03290.0293-0.02990.0614-0.01280.0653116.35747.7631-2.5789
36.96840.7401-3.76180.2865-0.55992.17390.1085-0.34710.08210.045-0.1818-0.116-0.13290.28030.07330.13060.0105-0.05840.14160.04170.153466.744776.50116.2531
44.89430.4843-0.44837.2117-1.41086.34080.0383-0.051-0.39070.06220.09250.50740.1988-0.2843-0.13080.05770.02130.02180.10860.00080.093840.92282.696512.7412
52.6227-3.93760.62017.8632-1.10371.52750.10650.098-0.089-0.1498-0.15460.30620.01-0.1440.04810.0237-0.0002-0.00770.0407-0.03760.065663.57349.57724.4567
65.5578-0.23061.2245.17031.14117.8666-0.0495-0.0725-0.3090.34610.109-0.59810.22050.3227-0.05950.11450.0182-0.05270.02860.01080.11267.662621.957410.401
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A608 - 658
2X-RAY DIFFRACTION1A2001 - 2002
3X-RAY DIFFRACTION2A659 - 723
4X-RAY DIFFRACTION2A2003 - 2004
5X-RAY DIFFRACTION3B608 - 658
6X-RAY DIFFRACTION3B2001 - 2002
7X-RAY DIFFRACTION4B659 - 723
8X-RAY DIFFRACTION4B2003 - 2004
9X-RAY DIFFRACTION5C608 - 658
10X-RAY DIFFRACTION5C2001 - 2002
11X-RAY DIFFRACTION6C659 - 723
12X-RAY DIFFRACTION6C2003 - 2004

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