[English] 日本語
Yorodumi
- PDB-6yjb: VcaM4I restriction endonuclease 5hmC-ssDNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yjb
TitleVcaM4I restriction endonuclease 5hmC-ssDNA complex
Components
  • DNA (5'-D(*CP*AP*(5HC)P*AP*G)-3')
  • HNH endonuclease
KeywordsHYDROLASE / PUA superfamily / EVE domain / DNA endonuclease / modification-dependent restriction endonuclease / MDRE / 5-methylcytosineE / 5-hydroxymethylcytosine / single stranded DNA
Function / homologyHNH endonuclease / HNH nuclease / endonuclease activity / DNA / HNH endonuclease
Function and homology information
Biological speciesVibrio campbellii (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsPastor, M. / Czapinska, H. / Lutz, T. / Helbrecht, I. / Xu, S. / Bochtler, M.
Citation
Journal: Nucleic Acids Res. / Year: 2021
Title: Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA.
Authors: Pastor, M. / Czapinska, H. / Helbrecht, I. / Krakowska, K. / Lutz, T. / Xu, S.Y. / Bochtler, M.
#1: Journal: Nucleic Acids Res. / Year: 2019
Title: A protein architecture guided screen for modification dependent restriction endonucleases.
Authors: Lutz, T. / Flodman, K. / Copelas, A. / Czapinska, H. / Mabuchi, M. / Fomenkov, A. / He, X. / Bochtler, M. / Xu, S.Y.
History
DepositionApr 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details
Revision 1.2Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HNH endonuclease
B: DNA (5'-D(*CP*AP*(5HC)P*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,86624
Polymers36,9102
Non-polymers1,95622
Water10,503583
1
A: HNH endonuclease
B: DNA (5'-D(*CP*AP*(5HC)P*AP*G)-3')
hetero molecules

A: HNH endonuclease
B: DNA (5'-D(*CP*AP*(5HC)P*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,73248
Polymers73,8194
Non-polymers3,91344
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/31
Buried area11870 Å2
ΔGint-297 kcal/mol
Surface area30490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.685, 128.685, 110.895
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-410-

GOL

21A-656-

HOH

31A-701-

HOH

41A-930-

HOH

-
Components

-
Protein / DNA chain , 2 types, 2 molecules AB

#1: Protein HNH endonuclease


Mass: 35390.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio campbellii (bacteria) / Gene: DSB67_20905 / Plasmid: pTXB1 (modified) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A344KQF3
#2: DNA chain DNA (5'-D(*CP*AP*(5HC)P*AP*G)-3')


Mass: 1519.052 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

-
Non-polymers , 4 types, 605 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 3.59 Å3/Da / Density % sol: 65.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Reservoir solution: 1.6 M (NH4)2SO4, 0.1 M MES pH 5.25; protein:DNA solution: 300 mM NaCl, 15 mM Tris-HCl pH 8.5 and 1mM TCEP. For cryo-protection the reservoir solution was diluted with ...Details: Reservoir solution: 1.6 M (NH4)2SO4, 0.1 M MES pH 5.25; protein:DNA solution: 300 mM NaCl, 15 mM Tris-HCl pH 8.5 and 1mM TCEP. For cryo-protection the reservoir solution was diluted with glycerol to achieve 30% concentration. 0.1 M spermine tetrahydrochloride was used as an additive.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 1.0064 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0064 Å / Relative weight: 1
ReflectionResolution: 1.55→29.77 Å / Num. obs: 78576 / % possible obs: 99.9 % / Redundancy: 39.2 % / Biso Wilson estimate: 30.8 Å2 / CC1/2: 1 / Rrim(I) all: 0.103 / Rsym value: 0.101 / Net I/σ(I): 26.96
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 39.9 % / Mean I/σ(I) obs: 1.96 / Num. unique obs: 12449 / CC1/2: 0.752 / Rrim(I) all: 2.364 / Rsym value: 2.334 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YEX

6yex


Resolution: 1.55→29.77 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.724 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.057
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED THE CONFORMATION OF TWO RESIDUES AT THE 5' END OF THE OLIGONUCLEOTIDE IS UNCERTAIN THE IDENTITY OF THE SOLVENT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED THE CONFORMATION OF TWO RESIDUES AT THE 5' END OF THE OLIGONUCLEOTIDE IS UNCERTAIN THE IDENTITY OF THE SOLVENT MOLECULES HAS BEEN ASSIGNED TENTATIVELY
RfactorNum. reflection% reflectionSelection details
Rfree0.1636 3912 5 %RANDOM
Rwork0.1425 ---
obs0.1436 74619 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.49 Å2 / Biso mean: 28.835 Å2 / Biso min: 16.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å2-0 Å2
3----1.22 Å2
Refinement stepCycle: final / Resolution: 1.55→29.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 101 121 585 3306
Biso mean--49.43 51.74 -
Num. residues----314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133109
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182688
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.6264257
X-RAY DIFFRACTIONr_angle_other_deg1.451.6146306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5345376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5123.659164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66415519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4571514
X-RAY DIFFRACTIONr_chiral_restr0.0710.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023506
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02658
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.276 294 -
Rwork0.258 5386 -
obs--99.44 %
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)
10.73560.1132-0.02680.0325-0.04680.420.00770.01490.07270.0008-0.00520.036-0.01980.0235-0.00250.0287-0.00730.00370.0473-0.00290.06935.6304-56.5878-19.4686
21.54150.1689-0.36160.2603-0.08540.53040.1291-0.10730.26390.0335-0.13230.0185-0.0109-0.0030.00310.0145-0.01890.01950.0806-0.03830.093734.1806-43.0633-6.1848
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 181
2X-RAY DIFFRACTION1B1 - 5
3X-RAY DIFFRACTION1C1 - 2000
4X-RAY DIFFRACTION1D1 - 2000
5X-RAY DIFFRACTION2A182 - 310
6X-RAY DIFFRACTION2E1 - 2000

+
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://pdbjlvh1.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