[English] 日本語
Yorodumi
- PDB-8gzl: Crystal structure of Cd2+-bound DNA aptamer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gzl
TitleCrystal structure of Cd2+-bound DNA aptamer
Components25-mer DNA
KeywordsDNA / DNA aptamer / Cd2+-binding / complex
Function / homology: / : / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGan, J.H. / Liu, H.H. / Gao, Y.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171197 China
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Crystal structures and identification of novel Cd2+-specific DNA aptamer.
Authors: Liu, H. / Gao, Y. / Mathivanan, J. / Armour-Garb, Z. / Shao, Z. / Zhang, Y. / Zhao, X. / Shao, Q. / Zhang, W. / Yang, J. / Cao, C. / Li, H. / Sheng, J. / Gan, J.
History
DepositionSep 27, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 25-mer DNA
B: 25-mer DNA
C: 25-mer DNA
D: 25-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,60411
Polymers30,7684
Non-polymers8377
Water543
1
A: 25-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0544
Polymers7,6921
Non-polymers3623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-12 kcal/mol
Surface area4860 Å2
MethodPISA
2
B: 25-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9423
Polymers7,6921
Non-polymers2502
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-12 kcal/mol
Surface area4800 Å2
MethodPISA
3
C: 25-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8042
Polymers7,6921
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area4780 Å2
MethodPISA
4
D: 25-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8042
Polymers7,6921
Non-polymers1121
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-8 kcal/mol
Surface area4730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.800, 45.690, 147.020
Angle α, β, γ (deg.)90.000, 92.870, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: DG / Beg label comp-ID: DG / End auth comp-ID: DC / End label comp-ID: DC / Auth seq-ID: 1 - 25 / Label seq-ID: 1 - 25

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

-
Components

#1: DNA chain
25-mer DNA


Mass: 7691.934 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 45% MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→29.37 Å / Num. obs: 6161 / % possible obs: 84.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 86.51 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.051 / Rrim(I) all: 0.118 / Net I/σ(I): 7.3 / Num. measured all: 30010 / Scaling rejects: 46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.184.40.45940969350.9760.2330.5181.881.7
9-29.374.80.05812492590.9970.030.06516.691.3

-
Processing

Software
NameVersionClassification
Aimless0.5.29data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GZJ

8gzj


Resolution: 3→29.37 Å / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 40.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2841 301 5.06 %
Rwork0.2334 5652 -
obs0.2362 5953 81.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 188.03 Å2 / Biso mean: 95.6236 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3→29.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2040 6 3 2049
Biso mean--110.39 30 -
Num. residues----101
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A984X-RAY DIFFRACTION17.078TORSIONAL
12B984X-RAY DIFFRACTION17.078TORSIONAL
13C984X-RAY DIFFRACTION17.078TORSIONAL
14D984X-RAY DIFFRACTION17.078TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.780.45371400.34152627276776
3.78-29.370.23871610.20373025318687
Refinement TLS params.Method: refined / Origin x: 4.7191 Å / Origin y: 9.3045 Å / Origin z: 38.6643 Å
111213212223313233
T0.9686 Å2-0.3438 Å2-0.1401 Å2-0.8816 Å20.0861 Å2--0.7641 Å2
L-0.2476 °2-0.5282 °20.1581 °2--0.1034 °20.0017 °2--0.1747 °2
S-0.1135 Å °0.0521 Å °-0.0457 Å °0.1996 Å °0.0889 Å °-0.0472 Å °-0.8263 Å °0.1028 Å °-0.0092 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 25
2X-RAY DIFFRACTION1allB1 - 25
3X-RAY DIFFRACTION1allC1 - 25
4X-RAY DIFFRACTION1allD1 - 25
5X-RAY DIFFRACTION1allE1 - 5
6X-RAY DIFFRACTION1allF1 - 2
7X-RAY DIFFRACTION1allG1 - 3

+
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