[English] 日本語
Yorodumi
- PDB-8kfs: Crystal structure of ZmMOC1/nicked Holliday junction complex at g... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8kfs
TitleCrystal structure of ZmMOC1/nicked Holliday junction complex at ground state
Components
  • DNA (25-MER)
  • DNA (33-MER)
  • DNA (5'-D(P*CP*AP*CP*GP*AP*TP*TP*G)-3')
  • Holliday junction resolvase MOC1, chloroplastic
KeywordsHYDROLASE / MOC1 / Holliday Junction / Time-resolved crystallography
Function / homologyHolliday junction resolvase MOC1-like / crossover junction DNA endonuclease activity / metal ion binding / DNA / DNA (> 10) / Holliday junction resolvase MOC1, chloroplastic
Function and homology information
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsZhang, D. / Luo, Z. / Lin, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971222 China
CitationJournal: Nat Commun / Year: 2024
Title: MOC1 cleaves Holliday junctions through a cooperative nick and counter-nick mechanism mediated by metal ions.
Authors: Zhang, D. / Xu, S. / Luo, Z. / Lin, Z.
History
DepositionAug 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Holliday junction resolvase MOC1, chloroplastic
B: Holliday junction resolvase MOC1, chloroplastic
C: DNA (33-MER)
D: DNA (25-MER)
E: DNA (5'-D(P*CP*AP*CP*GP*AP*TP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)55,4625
Polymers55,4625
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint-68 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.263, 78.028, 63.456
Angle α, β, γ (deg.)90.000, 98.115, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Holliday junction resolvase MOC1, chloroplastic


Mass: 17616.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 100192759 / Production host: Escherichia coli (E. coli) / References: UniProt: B4FCI7
#2: DNA chain DNA (33-MER)


Mass: 10137.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zea mays (maize)
#3: DNA chain DNA (25-MER)


Mass: 7665.932 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zea mays (maize)
#4: DNA chain DNA (5'-D(P*CP*AP*CP*GP*AP*TP*TP*G)-3')


Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Zea mays (maize)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 6% Isopropyl alcohol, 0.1 M Sodium acetate pH5.0, 35% Polyethylene glycol monomethyl ether 550

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 28620 / % possible obs: 97.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 13.02
Reflection shellResolution: 2.15→2.31 Å / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5689 / CC1/2: 0.837 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.21rc1_4958refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JRG

6jrg


Resolution: 2.15→19.51 Å / SU ML: 0.2741 / Cross valid method: FREE R-VALUE / σ(F): 1.64 / Phase error: 24.3234
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2275 1366 4.88 %
Rwork0.2031 26633 -
obs0.2043 27999 98.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.23 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 1345 0 62 3899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784064
X-RAY DIFFRACTIONf_angle_d0.88185799
X-RAY DIFFRACTIONf_chiral_restr0.053648
X-RAY DIFFRACTIONf_plane_restr0.007506
X-RAY DIFFRACTIONf_dihedral_angle_d23.55071565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.230.28131470.26722682X-RAY DIFFRACTION99.72
2.23-2.320.27711340.25472673X-RAY DIFFRACTION99.65
2.32-2.420.29961430.23542710X-RAY DIFFRACTION99.58
2.42-2.550.27461530.23212664X-RAY DIFFRACTION99.68
2.55-2.710.26431430.22492705X-RAY DIFFRACTION99.41
2.71-2.920.22021510.23812660X-RAY DIFFRACTION99.22
2.92-3.210.27781250.23372699X-RAY DIFFRACTION98.53
3.21-3.670.20591250.20532659X-RAY DIFFRACTION97.17
3.67-4.610.20771260.17332618X-RAY DIFFRACTION95.81
4.61-19.510.18431190.16522563X-RAY DIFFRACTION91.82

+
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