[English] 日本語
Yorodumi
- PDB-1em0: COMPLEX OF D(CCTAGG) WITH TETRA-[N-METHYL-PYRIDYL] PORPHYRIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1em0
TitleCOMPLEX OF D(CCTAGG) WITH TETRA-[N-METHYL-PYRIDYL] PORPHYRIN
ComponentsDNA (5'-D(*(CBR)P*CP*TP*AP*GP*G)-3')
KeywordsDNA / PORPHYRIN / RUFFLING / DNA DISTORTION / GROOVE BINDING
Function / homologyTETRA[N-METHYL-PYRIDYL] PORPHYRIN-NICKEL / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.9 Å
AuthorsNeidle, S. / Sanderson, M. / Bennett, M. / Krah, A. / Wien, F. / Garman, E. / McKenna, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: A DNA-porphyrin minor-groove complex at atomic resolution: the structural consequences of porphyrin ruffling.
Authors: Bennett, M. / Krah, A. / Wien, F. / Garman, E. / McKenna, R. / Sanderson, M. / Neidle, S.
History
DepositionMar 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*(CBR)P*CP*TP*AP*GP*G)-3')
B: DNA (5'-D(*(CBR)P*CP*TP*AP*GP*G)-3')
C: DNA (5'-D(*(CBR)P*CP*TP*AP*GP*G)-3')
D: DNA (5'-D(*(CBR)P*CP*TP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0728
Polymers7,5524
Non-polymers1,5204
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.210, 32.210, 62.257
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Cell settingtetragonal
Space group name H-MP41

-
Components

#1: DNA chain
DNA (5'-D(*(CBR)P*CP*TP*AP*GP*G)-3')


Mass: 1888.113 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PNI / TETRA[N-METHYL-PYRIDYL] PORPHYRIN-NICKEL


Mass: 735.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H36N8Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.25UM DNA, 1.25UM NI-PORPHYRIN, 50UM MGCL2, 5% MPD, 30MM SODIUM CACODYLATE, AGAINST 500UM RESERVOIR OF 55% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.25 mMDNA1drop
21.25 mMNi2+-TMPy1drop
350 mM1dropMgCl2
45 %MPD1drop
530 mMsodium cacodylate1drop
655 %MPD1reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF BM1410.9189
SYNCHROTRONEMBL/DESY, HAMBURG X1120.9057
Detector
TypeIDDetector
MARRESEARCH1IMAGE PLATE
MARRESEARCH2IMAGE PLATE
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91891
20.90571
ReflectionResolution: 0.86→30 Å / Num. obs: 45197 / % possible obs: 93 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.021
Reflection shellResolution: 0.9→1 Å / Redundancy: 8 % / Rmerge(I) obs: 0.124 / % possible all: 70.3
Reflection
*PLUS
Num. measured all: 336951

-
Processing

Software
NameVersionClassification
CCP4MAD PROGSmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(MAD PROGS)phasing
RefinementResolution: 0.9→6 Å / Num. parameters: 3867 / Num. restraintsaints: 0 / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2
Stereochemistry target values: NO RESTRAINTS USED, THEREFORE THE RMSD DEVIATIONS ABOVE DO NOT HAVE ANY MEANING
Details: FULL-MATRIX LEAST-SQUARES
RfactorNum. reflection% reflectionSelection details
Rfree0.172 2323 5 %RANDOM
Rwork0.152 ---
all0.151 42874 --
obs0.152 37075 --
Refinement stepCycle: LAST / Resolution: 0.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 772 196 202 1170
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 0.9 Å / Lowest resolution: 6 Å / σ(F): 4 / % reflection Rfree: 5 % / Rfactor obs: 0.142 / Rfactor Rfree: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.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

-
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