[English] 日本語
Yorodumi
- PDB-4j8x: X-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j8x
TitleX-ray structure of NCP145 with bound chlorido(eta-6-p-cymene)(N-fluorophenyl-2-pyridinecarbothioamide)ruthenium(II)
Components
  • (DNA) x 2
  • Histone H2A
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsSTRUCTURAL PROTEIN/DNA / nucleosome / histone / STRUCTURAL PROTEIN-DNA complex
Function / homology
Function and homology information


DNA-templated transcription, initiation / nucleosome / 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 signature. / Histone H2A conserved site / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A ...Histone, subunit A / Histone, subunit A / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. / Histone H2A conserved site / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Centromere kinetochore component CENP-T histone fold / CENP-T/Histone H4, histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF) / 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
Histone H4 / Histone H3.2 / Histone H2A type 1 / PARA-CYMENE RUTHENIUM CHLORIDE / Histone H2B 1.1 / DNA (> 100) / DNA (> 10) / DNA / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsAdhireksan, Z. / Davey, C.A.
CitationJournal: CHEM SCI / Year: 2013
Title: Novel metal(II) arene 2-pyridinecarbothioamides: a rationale to orally active organometallic anticancer agents
Authors: Meier, S.M. / Hanif, M. / Adhireksan, Z. / Pichler, V. / Novak, M. / Jirkovsky, E. / Jakupec, M.A. / Arion, V.B. / Davey, C.A. / Keppler, B.K. / Hartinger, C.G.
History
DepositionFeb 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
J: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,06016
Polymers198,13510
Non-polymers9256
Water0
1
A: Histone H3.2
B: Histone H4
C: Histone H2A
D: Histone H2B 1.1
I: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4747
Polymers99,0725
Non-polymers4022
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14780 Å2
ΔGint-133 kcal/mol
Surface area50640 Å2
MethodPISA
2
E: Histone H3.2
F: Histone H4
G: Histone H2A
H: Histone H2B 1.1
J: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5869
Polymers99,0635
Non-polymers5234
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15320 Å2
ΔGint-155 kcal/mol
Surface area51230 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58520 Å2
ΔGint-434 kcal/mol
Surface area73450 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)106.480, 109.820, 181.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
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) / Production host: Escherichia coli (E. coli) / 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) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A /


Mass: 13907.163 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6AZJ8, UniProt: P06897*PLUS
#4: Protein Histone H2B 1.1


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: hist1h2aj, LOC494591 / Production host: Escherichia coli (E. coli) / References: UniProt: P02281

-
DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA /


Mass: 44749.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA /


Mass: 44740.648 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 6 molecules

#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-RU7 / PARA-CYMENE RUTHENIUM CHLORIDE


Mass: 306.194 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14Cl2Ru
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

-
Details

Nonpolymer detailsCHLORIDO(ETA-6-P-CYMENE)(N-FLUOROPHENYL-2-PYRIDINECARBOTHIOAMIDE)RUTHENIUM(II) WAS USED IN ...CHLORIDO(ETA-6-P-CYMENE)(N-FLUOROPHENYL-2-PYRIDINECARBOTHIOAMIDE)RUTHENIUM(II) WAS USED IN CRYSTALLIZATION. HOWEVER, UPON REACTING WITH PROTEIN (HIS 79 CHAINS H,D), THE CL DEPARTED AND THE CARBOTHIAMIDE GROUP WAS CLEAVED OFF. THE REMAINING LIGAND IS DESCRIBED BY CHEMICAL COMPONENT RU7

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 40 mM MnCl2, 30 mM KCl, 20 mM K-Cacodylate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.5 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2011
RadiationMonochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.87→93.94 Å / Num. obs: 49232
Reflection shellResolution: 2.87→3.03 Å

-
Processing

Software
NameVersionClassification
RemDAqdata collection
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→93.94 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.87 / SU B: 17.483 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28015 1011 2.1 %RANDOM
Rwork0.23711 ---
obs0.23797 48147 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.532 Å2
Baniso -1Baniso -2Baniso -3
1-3.02 Å20 Å20 Å2
2---3.53 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.87→93.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6086 5939 38 0 12063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02112873
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4992.54618668
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9945757
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48621.255271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.586151183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9771586
X-RAY DIFFRACTIONr_chiral_restr0.0760.22119
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027635
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6721.53797
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.31626110
X-RAY DIFFRACTIONr_scbond_it1.44739076
X-RAY DIFFRACTIONr_scangle_it2.4564.512510
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.87→2.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 74 -
Rwork0.394 3393 -
obs--96.6 %

+
About Yorodumi

-
News

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more