[English] 日本語
Yorodumi
- PDB-2a2t: crystal structure of d(AAATATTT) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2a2t
Titlecrystal structure of d(AAATATTT)
Components5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
KeywordsDNA / AT / MN / CACODYLATE / HASO
Function / homologyCACODYLATE ION / : / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsValls, N. / Richter, M. / Subirana, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of a DNA duplex with all-AT base pairs.
Authors: Valls, N. / Richter, M. / Subirana, J.A.
History
DepositionJun 23, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 13, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_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.pdbx_dist_value / _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_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_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: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
G: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
B: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
H: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
C: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
I: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
D: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
J: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
E: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
K: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
F: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,82323
Polymers26,67111
Non-polymers1,15212
Water28816
1
A: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
G: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'


Theoretical massNumber of molelcules
Total (without water)4,8492
Polymers4,8492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
H: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'


Theoretical massNumber of molelcules
Total (without water)4,8492
Polymers4,8492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
I: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'


Theoretical massNumber of molelcules
Total (without water)4,8492
Polymers4,8492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
J: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9043
Polymers4,8492
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
K: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,94613
Polymers4,8492
Non-polymers1,09711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'

F: 5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'


Theoretical massNumber of molelcules
Total (without water)4,8492
Polymers4,8492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Unit cell
Length a, b, c (Å)147.623, 24.985, 82.139
Angle α, β, γ (deg.)90.00, 90.51, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: DNA chain
5'-D(*AP*AP*AP*TP*AP*TP*TP*T)-3'


Mass: 2424.641 Da / Num. of mol.: 11 / Source method: obtained synthetically
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, manganes chloride, spermine, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2manganes chloride11
3spermine11
4cacodylateCacodylic acid11
5HOH11
6MPD12
7manganes chloride12
8cacodylateCacodylic acid12
9HOH12

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.979433 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979433 Å / Relative weight: 1
ReflectionResolution: 3.1→15 Å / Num. obs: 5712 / Rsym value: 0.063
Reflection shellResolution: 3.1→3.21 Å / Rsym value: 0.184

-
Processing

Software
NameVersionClassification
REFMAC5.2.0016refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→15 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.889 / SU B: 47.705 / SU ML: 0.441 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R Free: 0.653 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.35737 269 4.7 %RANDOM
Rwork0.27216 ---
obs0.27587 5435 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.126 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å20 Å27.5 Å2
2--1.94 Å20 Å2
3----4.25 Å2
Refinement stepCycle: LAST / Resolution: 3.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1771 36 16 1823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212004
X-RAY DIFFRACTIONr_angle_refined_deg1.6533072
X-RAY DIFFRACTIONr_chiral_restr0.0650.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02924
X-RAY DIFFRACTIONr_nbd_refined0.1860.2801
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21120
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.254
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.27
X-RAY DIFFRACTIONr_scbond_it0.58432840
X-RAY DIFFRACTIONr_scangle_it1.0214.53072
LS refinement shellResolution: 3.1→3.177 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.491 21 -
Rwork0.361 373 -
obs--97.28 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8027-0.5941-4.70590.19581.550812.28490.0470.1270.0621-0.06120.5128-0.0677-0.6451-0.0693-0.55980.0104-0.00420.01520.04780.01820.029326.94010.325438.6891
27.2061.9926-4.73730.5861-1.75648.79360.33660.66610.2355-0.1976-0.0579-0.0189-0.0538-0.7553-0.27870.0935-0.00790.049-0.05060.009-0.021240.3987-0.534514.8865
33.2346-0.9697-3.48163.08291.291111.18140.32120.2710.0215-0.17810.1387-0.1976-0.22550.1271-0.45990.0142-0.07830.08260.1217-0.0654-0.037953.1296-0.3831-7.9656
415.40863.9982-11.77393.9548-0.584323.9906-0.0011-0.09490.32990.21940.27630.0301-0.20890.3454-0.2752-0.13270.02540.04250.02350.0429-0.123467.13070.4974-30.037
51.92910.2936-4.06480.0447-0.61868.56490.0645-0.0290.05380.0874-0.13240.0996-0.0885-0.61530.0679-0.08860.0394-0.01130.098-0.00020.091112.42930.09859.4747
615.1071.8148-12.1690.236-1.181514.1814-0.19330.74520.0328-0.23440.3461-0.07780.5053-0.1246-0.1528-0.0118-0.00130.0281-0.1179-0.01160.0064-2.47280.257582.2751
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1A - GA - B1 - 161 - 8
2X-RAY DIFFRACTION2B - HC - D1 - 161 - 8
3X-RAY DIFFRACTION3C - IE - F1 - 161 - 8
4X-RAY DIFFRACTION4D - JG - H1 - 161 - 8
5X-RAY DIFFRACTION5E - KI - J1 - 161 - 8
6X-RAY DIFFRACTION6FK1 - 81 - 8

+
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://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