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- PDB-1m19: LIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA -

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Basic information

Entry
Database: PDB / ID: 1m19
TitleLIGAND BINDING ALTERS THE STRUCTURE AND DYNAMICS OF NUCLEOSOMAL DNA
Components
  • Histone H2A type 1
  • Histone H2B
  • Histone H3.3C
  • Histone H4
  • Palindromic 146 Base Pair DNA Fragment
KeywordsSTRUCTURAL PROTEIN/DNA / nucleosome / chromatin / histone / pyrrole-imidazole polyamide / DNA regognition / chromatin remodeling / STRUCTURAL PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / protein heterodimerization activity / DNA binding / nucleus
Similarity search - Function
Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A ...Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
GAMMA-AMINO-BUTANOIC ACID / BETA-ALANINE / 3-AMINO-(DIMETHYLPROPYLAMINE) / 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID / : / 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID / DNA / DNA (> 10) / DNA (> 100) / Histone H2B ...GAMMA-AMINO-BUTANOIC ACID / BETA-ALANINE / 3-AMINO-(DIMETHYLPROPYLAMINE) / 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID / : / 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID / DNA / DNA (> 10) / DNA (> 100) / Histone H2B / Histone H4 / Histone H2B 1.1 / Histone H3.3C / Histone H2A type 1 / Histone H4
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSuto, R.K. / Edayathumangalam, R.S. / White, C.L. / Melander, C. / Gottesfeld, J.M. / Dervan, P.B. / Luger, K.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA-binding Ligands
Authors: Suto, R.K. / Edayathumangalam, R.S. / White, C.L. / Melander, C. / Gottesfeld, J.M. / Dervan, P.B. / Luger, K.
History
DepositionJun 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_distant_solvent_atoms / pdbx_entity_src_syn / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN THE PYRROLE-IMIDAZOLE POLYAMIDE CONSISTS OF THE FOLLOWING GROUPS LINKED BY PEPTIDE BONDS. ...HETEROGEN THE PYRROLE-IMIDAZOLE POLYAMIDE CONSISTS OF THE FOLLOWING GROUPS LINKED BY PEPTIDE BONDS. IMT-PYB-PYB-PYB-ABU-PYB-PYB-PYB-PYB-BAL-DIB IMT = 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID PYB = 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID ABU = GAMMA-AMINO-BUTANOIC ACID; GAMMA(AMINO)-BUTYRIC ACID BAL = BETA-ALANINE DIB = 3-AMINO-(DIMETHYLPROPYLAMINE)
Remark 999SEQUENCE AUTHOR INDICATES ARG-SER DISCREPANCY AT RESIDUE 86 IS A CONFLICT BETWEEN SEQUENCE AND ...SEQUENCE AUTHOR INDICATES ARG-SER DISCREPANCY AT RESIDUE 86 IS A CONFLICT BETWEEN SEQUENCE AND SEQUENCE DATABASE REFERENCE SWISSPROT ENTRY P02302. SER WAS CRYSTALLIZED AT POSITION 486,686 FOR CHAINS A,E. AUTHOR INFORMS GLY-ARG MISMATCH AT RESIDUE 899,1099 (CHAINS C,G) AND SER-THR MISMATCH AT RESIDUE 1229,1429 (CHAINS D,H) ARE VARIANTS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Palindromic 146 Base Pair DNA Fragment
J: Palindromic 146 Base Pair DNA Fragment
A: Histone H3.3C
B: Histone H4
C: Histone H2A type 1
D: Histone H2B
E: Histone H3.3C
F: Histone H4
G: Histone H2A type 1
H: Histone H2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,58476
Polymers198,89710
Non-polymers7,68766
Water11,836657
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.045, 109.662, 183.018
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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DNA chain , 1 types, 2 molecules IJ

#1: DNA chain Palindromic 146 Base Pair DNA Fragment


Mass: 45054.844 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

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Protein , 4 types, 8 molecules AEBFCGDH

#2: Protein Histone H3.3C


Mass: 15320.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: h3-5 / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P02302
#3: Protein Histone H4 /


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC121398084 / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8J1LTD2, UniProt: P62799*PLUS
#4: Protein Histone H2A type 1


Mass: 13962.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#5: Protein Histone H2B /


Mass: 13848.097 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC108704303 / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8J0U496, UniProt: P02281*PLUS

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Non-polymers , 7 types, 723 molecules

#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mn
#7: Chemical
ChemComp-IMT / 4-AMINO-(1-METHYLIMIDAZOLE)-2-CARBOXYLIC ACID


Mass: 141.128 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H7N3O2
#8: Chemical...
ChemComp-PYB / 4-AMINO-(1-METHYLPYRROLE)-2-CARBOXYLIC ACID


Mass: 140.140 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C6H8N2O2
#9: Chemical
ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID / Γ-Aminobutyric acid


Mass: 103.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H9NO2 / Comment: neurotransmitter, inhibitor*YM
#10: Chemical
ChemComp-BAL / BETA-ALANINE / Β-Alanine


Type: peptide-like / Mass: 89.093 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H7NO2
#11: Chemical
ChemComp-DIB / 3-AMINO-(DIMETHYLPROPYLAMINE) / Dimethylaminopropylamine


Mass: 102.178 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H14N2
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 657 / 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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Manganese chloride, potassium chloride, potassium cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Method: vapor diffusion / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
140-45 mM1reservoirMnCl2
235-38.8 mM1reservoirKCl
320 mMpotassium cacodylate1droppH6.0
44 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→80 Å / Num. all: 96437 / Num. obs: 93443 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.4
Reflection shellHighest resolution: 2.3 Å / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 2.2 / % possible all: 93.6
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 80 Å / % possible obs: 99 %
Reflection shell
*PLUS
% possible obs: 93.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AOI

1aoi


Resolution: 2.3→80 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 2825 -random
Rwork0.2139 ---
all-96250 --
obs-93443 97.1 %-
Refinement stepCycle: LAST / Resolution: 2.3→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6065 5980 456 657 13158
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 80 Å / Num. reflection all: 96437 / Num. reflection obs: 93612 / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.39

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