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- PDB-4n4g: Crystal structure of the Bromo-PWWP of the mouse zinc finger MYND... -

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Basic information

Entry
Database: PDB / ID: 4n4g
TitleCrystal structure of the Bromo-PWWP of the mouse zinc finger MYND-type containing 11 isoform alpha
ComponentsZinc finger MYND domain-containing protein 11
KeywordsTRANSCRIPTION / tandem bromodomain-zinc finger-PWWP motif / histone H3.3-specific
Function / homology
Function and homology information


regulation of transcription elongation by RNA polymerase II / negative regulation of JNK cascade / regulation of signal transduction / negative regulation of canonical NF-kappaB signal transduction / methylated histone binding / negative regulation of extrinsic apoptotic signaling pathway / transcription corepressor activity / chromosome / chromatin organization / histone binding ...regulation of transcription elongation by RNA polymerase II / negative regulation of JNK cascade / regulation of signal transduction / negative regulation of canonical NF-kappaB signal transduction / methylated histone binding / negative regulation of extrinsic apoptotic signaling pathway / transcription corepressor activity / chromosome / chromatin organization / histone binding / double-stranded DNA binding / defense response to virus / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / : / : / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / SH3 type barrels. - #140 / domain with conserved PWWP motif ...: / : / : / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Zinc finger MYND domain-containing protein 11
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.947 Å
AuthorsLi, Y. / Ren, Y. / Li, H.
CitationJournal: Nature / Year: 2014
Title: ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression
Authors: Wen, H. / Li, Y. / Xi, Y. / Jiang, S. / Stratton, S. / Peng, D. / Tanaka, K. / Ren, Y. / Xia, Z. / Wu, J. / Li, B. / Barton, M.C. / Li, W. / Li, H. / Shi, X.
History
DepositionOct 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_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

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Assembly

Deposited unit
A: Zinc finger MYND domain-containing protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7663
Polymers29,6061
Non-polymers1602
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.919, 64.267, 75.587
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Zinc finger MYND domain-containing protein 11 / Adenovirus 5 E1A-binding protein / Protein BS69


Mass: 29605.783 Da / Num. of mol.: 1 / Fragment: UNP residues 154-371
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: BS69, Zmynd11 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8R5C8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Mosaicity: 0.42 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 8% (w/v) polyethylene glycol 3000, 0.1M Imidazole, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1.2825 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 14, 2012 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2825 Å / Relative weight: 1
ReflectionResolution: 1.947→50 Å / Num. all: 37810 / Num. obs: 37810 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.081 / Χ2: 1.232 / Net I/σ(I): 19.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.947-1.986.10.78618780.8181100
1.98-2.026.20.55618880.792199.9
2.02-2.066.20.45419000.8251100
2.06-2.16.30.42118920.9121100
2.1-2.156.20.32818830.8491100
2.15-2.26.30.2918840.8841100
2.2-2.256.20.32818761.8161100
2.25-2.316.20.3219031.6031100
2.31-2.386.30.18918990.9741100
2.38-2.466.40.18418750.9711100
2.46-2.546.40.1518881.0091100
2.54-2.656.40.13319161.0511100
2.65-2.776.40.11418851.131100
2.77-2.916.50.09319071.1351100
2.91-3.16.50.07818681.2471100
3.1-3.336.50.06418941.4451100
3.33-3.676.50.05718991.8081100
3.67-4.26.50.05118871.9641100
4.2-5.296.50.04318931.7541100
5.29-506.40.0418951.56199.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.947→31.134 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8453 / SU ML: 0.21 / σ(F): 1.91 / Phase error: 22.25 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F(I)_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 1946 5.17 %RANDOM
Rwork0.188 ---
obs0.1899 37651 99.61 %-
all-37810 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.77 Å2 / Biso mean: 31.7489 Å2 / Biso min: 8.38 Å2
Refinement stepCycle: LAST / Resolution: 1.947→31.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 6 167 1929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051811
X-RAY DIFFRACTIONf_angle_d0.9242437
X-RAY DIFFRACTIONf_chiral_restr0.066242
X-RAY DIFFRACTIONf_plane_restr0.004313
X-RAY DIFFRACTIONf_dihedral_angle_d14.98678
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9473-1.9960.28391500.24612493264399
1.996-2.050.2481390.220825432682100
2.05-2.11030.23771340.205625962730100
2.1103-2.17840.24651590.208525482707100
2.1784-2.25620.29841330.27662478261198
2.2562-2.34650.29391580.23442522268098
2.3465-2.45330.24731310.203125442675100
2.4533-2.58260.24461740.201425372711100
2.5826-2.74430.21751610.188325602721100
2.7443-2.9560.21311280.182725392667100
2.956-3.25320.1941350.180525952730100
3.2532-3.72330.19911120.165325772689100
3.7233-4.68840.18371280.156125832711100
4.6884-31.13770.2391040.182525902694100

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