[English] 日本語
Yorodumi
- PDB-6qm2: NlaIV restriction endonuclease -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qm2
TitleNlaIV restriction endonuclease
ComponentsType-2 restriction enzyme NlaIV
KeywordsHYDROLASE / RESTRICTION ENDONUCLEASE / NLAIV / BLUNT END CUTTER
Function / homologyType-2 restriction enzyme NlaIV / NgoBV restriction endonuclease / type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / : / Type II restriction enzyme NlaIV
Function and homology information
Biological speciesNeisseria lactamica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsCzapinska, H. / Siwek, W. / Szczepanowski, R.H. / Bujnicki, J.M. / Bochtler, M. / Skowronek, K.
Citation
Journal: J.Mol.Biol. / Year: 2019
Title: Crystal Structure and Directed Evolution of Specificity of NlaIV Restriction Endonuclease.
Authors: Czapinska, H. / Siwek, W. / Szczepanowski, R.H. / Bujnicki, J.M. / Bochtler, M. / Skowronek, K.J.
#1: Journal: Protein Eng. Des. Sel. / Year: 2005
Title: A theoretical model of restriction endonuclease NlaIV in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis and circular dichroism spectroscopy.
Authors: Chmiel, A.A. / Radlinska, M. / Pawlak, S.D. / Krowarsch, D. / Bujnicki, J.M. / Skowronek, K.J.
History
DepositionFeb 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type-2 restriction enzyme NlaIV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2163
Polymers29,1541
Non-polymers622
Water2,216123
1
A: Type-2 restriction enzyme NlaIV
hetero molecules

A: Type-2 restriction enzyme NlaIV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4316
Polymers58,3072
Non-polymers1244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area3490 Å2
ΔGint-44 kcal/mol
Surface area24770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.380, 110.380, 209.006
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

-
Components

#1: Protein Type-2 restriction enzyme NlaIV / R.NlaIV / Endonuclease NlaIV / Type II restriction enzyme NlaIV


Mass: 29153.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria lactamica (bacteria) / Strain: NRCC 2118 / Gene: nlaIVR / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: P50183, type II site-specific deoxyribonuclease
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 10 mg/ml of the enzyme in 15 % glycerol, 50 mM NaOH/HEPES pH 7,5, 50 mM KCl, 10 mM DTT and 5 mM CaCl2 was mixed in 1:1 ratio with double stranded DNA composed of the 5'-ATGGTACCTGC-3' and 5'- ...Details: 10 mg/ml of the enzyme in 15 % glycerol, 50 mM NaOH/HEPES pH 7,5, 50 mM KCl, 10 mM DTT and 5 mM CaCl2 was mixed in 1:1 ratio with double stranded DNA composed of the 5'-ATGGTACCTGC-3' and 5'-CAGGTACCATG-3' strands. The protein-DNA solutions were in turn mixed in 1:1 ratio with the precipitant solution containing 2 M NaCl and 100 mM citric acid, pH 5.
PH range: 5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 17, 2008 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 18997 / % possible obs: 98.5 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.043 / Rsym value: 0.04 / Net I/σ(I): 28.92
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 1.72 / Rsym value: 0.986 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
STARANISOdata scaling
autoSHARPphasing
SHELXDEphasing
SOLOMONphasing
DMphasing
PARROTphasing
ARP/wARPmodel building
BUCCANEERmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.8→29.72 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 11.197 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.221
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The ION IDENTITY HAS BEEN ASSIGNED TENTATIVELY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22103 912 4.8 %RANDOM
Rwork0.19095 ---
obs0.19245 18083 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 115.889 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20.84 Å20 Å2
2--1.68 Å2-0 Å2
3----5.44 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 2 123 2181
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192142
X-RAY DIFFRACTIONr_bond_other_d0.0010.021994
X-RAY DIFFRACTIONr_angle_refined_deg1.0831.9362893
X-RAY DIFFRACTIONr_angle_other_deg0.84934637
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2895253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83424.352108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63915405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2891512
X-RAY DIFFRACTIONr_chiral_restr0.0620.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022365
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02455
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_it3.82511.6481003
X-RAY DIFFRACTIONr_mcbond_other3.81411.6431002
X-RAY DIFFRACTIONr_mcangle_it6.42717.4821259
X-RAY DIFFRACTIONr_mcangle_other6.42717.4891260
X-RAY DIFFRACTIONr_scbond_it3.76511.8941139
X-RAY DIFFRACTIONr_scbond_other3.76511.8931139
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.54217.6321634
X-RAY DIFFRACTIONr_long_range_B_refined9.963127.8012402
X-RAY DIFFRACTIONr_long_range_B_other9.927127.7342390
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 54 -
Rwork0.392 1305 -
obs--98.48 %

+
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