[English] 日本語
Yorodumi
- PDB-6kvo: Crystal structure of chloroplast resolvase in complex with Hollid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kvo
TitleCrystal structure of chloroplast resolvase in complex with Holliday junction
Components
  • DNA (5'-D(*AP*CP*AP*AP*CP*AP*GP*AP*TP*GP*AP*TP*GP*GP*AP*GP*CP*T)-3')
  • DNA (5'-D(*GP*CP*CP*TP*TP*GP*CP*TP*TP*GP*GP*AP*CP*AP*TP*CP*TP*T)-3')
  • DNA (5'-D(P*AP*AP*GP*AP*TP*GP*TP*CP*CP*AP*TP*CP*TP*GP*TP*TP*GP*T)-3')
  • DNA (5'-D(P*AP*GP*CP*TP*CP*CP*AP*TP*CP*AP*AP*GP*CP*AP*AP*GP*GP*C)-3')
  • NtMOC1
KeywordsPLANT PROTEIN/DNA / chloroplast / resolvase / Holliday junction / PLANT PROTEIN / PLANT PROTEIN-DNA complex
Function / homologyHolliday junction resolvase MOC1-like / crossover junction DNA endonuclease activity / metal ion binding / DNA / DNA (> 10) / Uncharacterized protein LOC107823122
Function and homology information
Biological speciesNicotiana tabacum (common tobacco)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYan, J.J. / Hong, S.X. / Guan, Z.Y. / Yin, P.
CitationJournal: Nat Commun / Year: 2020
Title: Structural insights into sequence-dependent Holliday junction resolution by the chloroplast resolvase MOC1.
Authors: Yan, J. / Hong, S. / Guan, Z. / He, W. / Zhang, D. / Yin, P.
History
DepositionSep 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NtMOC1
B: NtMOC1
C: DNA (5'-D(*AP*CP*AP*AP*CP*AP*GP*AP*TP*GP*AP*TP*GP*GP*AP*GP*CP*T)-3')
D: DNA (5'-D(*GP*CP*CP*TP*TP*GP*CP*TP*TP*GP*GP*AP*CP*AP*TP*CP*TP*T)-3')
E: DNA (5'-D(P*AP*GP*CP*TP*CP*CP*AP*TP*CP*AP*AP*GP*CP*AP*AP*GP*GP*C)-3')
F: DNA (5'-D(P*AP*AP*GP*AP*TP*GP*TP*CP*CP*AP*TP*CP*TP*GP*TP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,51510
Polymers59,2746
Non-polymers2414
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11520 Å2
ΔGint-151 kcal/mol
Surface area24900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.316, 92.155, 65.894
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein NtMOC1


Mass: 18605.326 Da / Num. of mol.: 2 / Mutation: Q162K,E235Q,E239Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: LOC107823122 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1S4CVP6

-
DNA chain , 4 types, 4 molecules CDEF

#2: DNA chain DNA (5'-D(*AP*CP*AP*AP*CP*AP*GP*AP*TP*GP*AP*TP*GP*GP*AP*GP*CP*T)-3')


Mass: 5573.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*CP*TP*TP*GP*CP*TP*TP*GP*GP*AP*CP*AP*TP*CP*TP*T)-3')


Mass: 5473.538 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*AP*GP*CP*TP*CP*CP*AP*TP*CP*AP*AP*GP*CP*AP*AP*GP*GP*C)-3')


Mass: 5494.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(P*AP*AP*GP*AP*TP*GP*TP*CP*CP*AP*TP*CP*TP*GP*TP*TP*GP*T)-3')


Mass: 5521.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 3 types, 51 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: Sodium acetate trihydrate, PEG 3350, Tacsimate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.5→49.03 Å / Num. obs: 26297 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 70.19 Å2 / CC1/2: 0.954 / Rmerge(I) obs: 0.252 / Rpim(I) all: 0.108 / Rrim(I) all: 0.275 / Net I/σ(I): 5.3
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2898 / CC1/2: 0.891 / Rpim(I) all: 0.21 / Rrim(I) all: 0.549 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX1.14rc3_3206refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→31.02 Å / SU ML: 0.3287 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.4468 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2343 1305 4.97 %
Rwork0.2019 24931 -
obs0.2035 26236 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.72 Å2
Refinement stepCycle: LAST / Resolution: 2.5→31.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 1468 0 47 4007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814197
X-RAY DIFFRACTIONf_angle_d0.94025994
X-RAY DIFFRACTIONf_chiral_restr0.0568661
X-RAY DIFFRACTIONf_plane_restr0.0067510
X-RAY DIFFRACTIONf_dihedral_angle_d24.10662210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.34381490.27182695X-RAY DIFFRACTION98.89
2.6-2.720.31091410.26822744X-RAY DIFFRACTION100
2.72-2.860.31311170.26252749X-RAY DIFFRACTION99.97
2.86-3.040.27071570.25242714X-RAY DIFFRACTION100
3.04-3.270.26881430.23832743X-RAY DIFFRACTION99.9
3.27-3.60.2091330.20262786X-RAY DIFFRACTION100
3.6-4.120.24431670.20132773X-RAY DIFFRACTION100
4.12-5.190.21821420.17112815X-RAY DIFFRACTION99.97
5.19-31.020.20651560.18622912X-RAY DIFFRACTION99.1
Refinement TLS params.Method: refined / Origin x: 27.0730554385 Å / Origin y: 16.7948053602 Å / Origin z: 18.1283811642 Å
111213212223313233
T0.346189180636 Å20.0132301365013 Å20.0328047822879 Å2-0.371642825595 Å2-0.00754458434689 Å2--0.383659106659 Å2
L2.12867476048 °20.565187388032 °20.498563673245 °2-3.32755729251 °2-0.190038942948 °2--2.54839233146 °2
S-0.0419655307852 Å °0.162093317283 Å °0.0848241919618 Å °0.138576099535 Å °0.199046432792 Å °-0.0287261905544 Å °0.0603765312001 Å °-0.0617971024292 Å °-0.112662973069 Å °
Refinement TLS groupSelection details: all

+
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