[English] 日本語
Yorodumi
- PDB-9k8p: Crystal structure of a short zinc-dependent DNAzyme minGAA, dimer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9k8p
TitleCrystal structure of a short zinc-dependent DNAzyme minGAA, dimeric form
ComponentsDNAzyme minGAA
KeywordsDNA-RNA HYBRID / DNAzyme / RNA cleavage / Zinc-dependent
Function / homologyDNA/RNA hybrid / DNA/RNA hybrid (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsYamasaki, K. / Yamasaki, T. / Kubota, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A minimal Zn2+-dependent RNA-cleaving DNAzyme and its B-DNA-like crystal and solution structures
Authors: Yamasaki, K. / Inomata, R. / Yamasaki, T. / Kubota, T. / Miyashita, N. / Takeuchi, K. / Miyagishi, M.
History
DepositionOct 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNAzyme minGAA
B: DNAzyme minGAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4506
Polymers16,1882
Non-polymers2624
Water1086
1
A: DNAzyme minGAA
hetero molecules

A: DNAzyme minGAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4506
Polymers16,1882
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4580 Å2
ΔGint-102 kcal/mol
Surface area8760 Å2
MethodPISA
2
B: DNAzyme minGAA
hetero molecules

B: DNAzyme minGAA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4506
Polymers16,1882
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4470 Å2
ΔGint-97 kcal/mol
Surface area8640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.096, 50.382, 51.382
Angle α, β, γ (deg.)90.00, 106.95, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: DNA/RNA hybrid DNAzyme minGAA


Mass: 8094.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 6.75% 2-methyl-2,4-pentandiol (MPD), 50 mM guanidine hydrochloride, 18 mM HEPES (7.5), 5.4 mM spermine, 18 mM LiCl, 36 mM SrCl2, 4.5 mM MgCl2, and 1 mM ZnCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.08 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.85→49.16 Å / Num. obs: 3855 / % possible obs: 92.6 % / Redundancy: 3.38 % / CC1/2: 0.997 / Rmerge(I) obs: 0.042 / Net I/σ(I): 9.4
Reflection shellResolution: 2.85→3.02 Å / Redundancy: 1.69 % / Rmerge(I) obs: 0.7 / Num. unique obs: 1071 / CC1/2: 0.649 / % possible all: 85.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→49.15 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.929 / SU B: 26.7 / SU ML: 0.521 / Cross valid method: THROUGHOUT / ESU R Free: 0.529 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32929 193 5 %RANDOM
Rwork0.24316 ---
obs0.24784 3661 97.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 108.704 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20.01 Å2
2---0.41 Å20 Å2
3---0.1 Å2
Refinement stepCycle: 1 / Resolution: 2.85→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1061 4 6 1071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0111228
X-RAY DIFFRACTIONr_bond_other_d0.0030.02586
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.1781898
X-RAY DIFFRACTIONr_angle_other_deg1.5962.9791386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02665
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02300
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it10.63511.2731226
X-RAY DIFFRACTIONr_scbond_other10.62811.2691222
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.08616.891892
X-RAY DIFFRACTIONr_long_range_B_refined18.6961733
X-RAY DIFFRACTIONr_long_range_B_other18.6911734
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.852→2.926 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.745 13 -
Rwork0.51 247 -
obs--93.19 %

+
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