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- PDB-3mnn: A Ruthenium Antitumour Agent Forms Specific Histone Protein Adduc... -

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Basic information

Entry
Database: PDB / ID: 3mnn
TitleA Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core
Components
  • (DNA (145-MER)) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / NUCLEOSOME / NCP / RUTHENIUM / RAPTA-C / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


structural constituent of chromatin / nucleosome / nucleosome assembly / protein heterodimerization activity / DNA binding / nucleoplasm / 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. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / 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
1-methyl-4-(1-methylethyl)benzene / Chem-PTW / RUTHENIUM ION / DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOng, M.S. / Davey, C.A.
CitationJournal: Chemistry / Year: 2011
Title: A ruthenium antimetastasis agent forms specific histone protein adducts in the nucleosome core
Authors: Wu, B. / Ong, M.S. / Groessl, M. / Adhireksan, Z. / Hartinger, C.G. / Dyson, P.J. / Davey, C.A.
History
DepositionApr 22, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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_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_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_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: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
I: DNA (145-MER)
J: DNA (145-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,69323
Polymers196,20310
Non-polymers1,49013
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area57000 Å2
ΔGint-382 kcal/mol
Surface area73670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.350, 109.860, 182.590
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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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3.2


Mass: 15303.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: HISTONE H3 / Plasmid: pET3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P84233
#2: 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: HISTONE H4 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P62799
#3: Protein Histone H2A


Mass: 12941.095 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: HISTONE H2A, LOC494591 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#4: Protein Histone H2B 1.1 / H2B1.1


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: HISTONE H2B / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P02281

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (145-MER)


Mass: 44749.664 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: PALINDROMIC ALPHA-SATELLITE 145 BASE PAIR DNA CLONED AS TWO HALF-SITES IN pUC19 PLASMID, EXPRESSED IN E. COLI HB101 CELLS.
#6: DNA chain DNA (145-MER)


Mass: 44740.648 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: PALINDROMIC ALPHA-SATELLITE 145 BASE PAIR DNA CLONED AS TWO HALF-SITES IN pUC19 PLASMID, EXPRESSED IN E. COLI HB101 CELLS.

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Non-polymers , 6 types, 35 molecules

#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-RU / RUTHENIUM ION


Mass: 101.070 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ru
#10: Chemical ChemComp-MML / 1-methyl-4-(1-methylethyl)benzene / p-cymene


Mass: 134.218 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14
#11: Chemical ChemComp-PTW / 1,3,5-triaza-7-phosphatricyclo[3.3.1.1~3,7~]decane / 1,3,5-Triaza-7-phosphaadamantane


Mass: 157.153 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12N3P
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE RUTHENIUM ANTITUMOUR AGENT RAPTA-C CONSISTS OF RU, MML, PTW AND TWO CL BINDING TO THE RU ATOM. ...THE RUTHENIUM ANTITUMOUR AGENT RAPTA-C CONSISTS OF RU, MML, PTW AND TWO CL BINDING TO THE RU ATOM. THE CL ATOMS AT RU WERE SUBSTITUTED WITH OTHER PROTEIN GROUPS ON BINDING.
Sequence detailsG102A IN ENTITY 1 (CHAIN A AND E) AND S29T IN ENTITY 4 (CHAIN D AND H) REPRESENT UNINTENTIONAL ...G102A IN ENTITY 1 (CHAIN A AND E) AND S29T IN ENTITY 4 (CHAIN D AND H) REPRESENT UNINTENTIONAL MUTATIONS OR VARIATION IN GENOMIC SOURCES.

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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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: 55mM KCl, 85mM MnCl2, 20mM K-Cacodylate, pH 6, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.5 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.5→94.13 Å / Num. obs: 74426 / % possible obs: 99.7 % / Redundancy: 4.4 % / Biso Wilson estimate: 72 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 1.7 / Num. unique all: 10557 / % possible all: 98.2

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASESphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NZD

2nzd


Resolution: 2.5→94.13 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.929 / SU B: 11.557 / SU ML: 0.258 / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27704 1485 2 %RANDOM
Rwork0.24747 ---
all0.2475 74426 --
obs0.24809 72837 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.801 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2---2.19 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.5→94.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6086 5939 79 22 12126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02112928
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4752.54818773
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0855757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26121.255271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55151183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2161586
X-RAY DIFFRACTIONr_chiral_restr0.1350.22131
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027675
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.24988
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.28076
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2383
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1530.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7171.53871
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.326110
X-RAY DIFFRACTIONr_scbond_it1.097312173
X-RAY DIFFRACTIONr_scangle_it1.9794.512591
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 105 -
Rwork0.367 5150 -
obs--96.78 %

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