[English] 日本語
Yorodumi
- PDB-4rd5: Crystal structure of R.NgoAVII restriction endonuclease B3 domain... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rd5
TitleCrystal structure of R.NgoAVII restriction endonuclease B3 domain with cognate DNA
Components
  • DNA (5'-D(*CP*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*AP*TP*TP*GP*CP*CP*GP*CP*TP*TP*AP*GP*G)-3')
  • Restriction endonuclease R.NgoVII
KeywordsHYDROLASE/DNA / restriction endonuclease / B3 DNA binding domain / protein-DNA complex / HYDROLASE-DNA complex
Function / homologyRestriction endonuclease, type II, NgoFVII / : / NgoFVII restriction endonuclease N-terminal PLD domain / NgoFVII C-terminal B3-like DNA-binding domain / endonuclease activity / DNA / DNA (> 10) / Restriction endonuclease NgoFVII
Function and homology information
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsTamulaitiene, G. / Silanskas, A. / Grazulis, S. / Zaremba, M. / Siksnys, V.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Crystal structure of the R-protein of the multisubunit ATP-dependent restriction endonuclease NgoAVII.
Authors: Tamulaitiene, G. / Silanskas, A. / Grazulis, S. / Zaremba, M. / Siksnys, V.
History
DepositionSep 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Restriction endonuclease R.NgoVII
B: Restriction endonuclease R.NgoVII
C: DNA (5'-D(*CP*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)-3')
D: DNA (5'-D(*GP*GP*GP*AP*TP*TP*GP*CP*CP*GP*CP*TP*TP*AP*GP*G)-3')
E: DNA (5'-D(*CP*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)-3')
F: DNA (5'-D(*GP*GP*GP*AP*TP*TP*GP*CP*CP*GP*CP*TP*TP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)60,9296
Polymers60,9296
Non-polymers00
Water1,54986
1
A: Restriction endonuclease R.NgoVII
C: DNA (5'-D(*CP*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)-3')
D: DNA (5'-D(*GP*GP*GP*AP*TP*TP*GP*CP*CP*GP*CP*TP*TP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)30,4643
Polymers30,4643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-21 kcal/mol
Surface area12210 Å2
MethodPISA
2
B: Restriction endonuclease R.NgoVII
E: DNA (5'-D(*CP*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)-3')
F: DNA (5'-D(*GP*GP*GP*AP*TP*TP*GP*CP*CP*GP*CP*TP*TP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)30,4643
Polymers30,4643
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-22 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.414, 88.414, 152.437
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-455-

HOH

-
Components

#1: Protein Restriction endonuclease R.NgoVII


Mass: 20666.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: ATCC 700825 / FA 1090 / Gene: NGO0364 / Plasmid: pLATE31 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q5F9M9, type II site-specific deoxyribonuclease
#2: DNA chain DNA (5'-D(*CP*CP*CP*TP*AP*AP*GP*CP*GP*GP*CP*AP*AP*TP*CP*C)-3')


Mass: 4828.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct
#3: DNA chain DNA (5'-D(*GP*GP*GP*AP*TP*TP*GP*CP*CP*GP*CP*TP*TP*AP*GP*G)-3')


Mass: 4970.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic construct
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystallization buffer was 0.1 M MES-imidazole pH 6.5, 12.5% w/v PEG1000, 12.5% w/v PEG3350, 12.5% MPD, 0.02 M of each Glu, Ala, Gly, Lys, Ser, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 21, 2013
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→152.437 Å / Num. all: 17327 / Num. obs: 17327 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.1 % / Biso Wilson estimate: 33.45 Å2 / Rsym value: 0.097 / Net I/σ(I): 32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.7-2.8518.60.3451.94599424790.345100
2.85-3.0220.30.2662.44706423160.266100
3.02-3.2320.10.1743.64429422000.174100
3.23-3.4919.40.1125.64017620710.112100
3.49-3.8218.90.0973604519110.09100
3.82-4.27200.0748.53467317370.074100
4.27-4.9318.90.0659.42969115680.065100
4.93-6.0417.80.069.82352113220.06100
6.04-8.5418.20.0598.51944610670.059100
8.54-152.43714.80.0566.797336560.05699.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å76.48 Å
Translation4 Å76.48 Å

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
MOLREP6phasing
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.15data extraction
MxCuBEdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→48.337 Å / SU ML: 0.33 / σ(F): 1.67 / Phase error: 24.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 3242 10.23 %RANDOM
Rwork0.2138 ---
all0.2175 17327 --
obs0.2175 17265 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.36 Å2 / Biso mean: 36.24 Å2 / Biso min: 5.23 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.337 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 1224 0 86 3793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063923
X-RAY DIFFRACTIONf_angle_d0.7945566
X-RAY DIFFRACTIONf_chiral_restr0.041606
X-RAY DIFFRACTIONf_plane_restr0.005512
X-RAY DIFFRACTIONf_dihedral_angle_d24.051496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.74030.25341580.249512331391100
2.7403-2.78310.30481330.262412511384100
2.7831-2.82880.34661640.262711931357100
2.8288-2.87750.32051400.248812261366100
2.8775-2.92980.23781580.264412431401100
2.9298-2.98620.27791260.249312551381100
2.9862-3.04710.32741300.260412611391100
3.0471-3.11340.32721600.249211851345100
3.1134-3.18580.27881290.235612841413100
3.1858-3.26540.2131250.229412301355100
3.2654-3.35370.24121390.201512231362100
3.3537-3.45240.25861500.21412341384100
3.4524-3.56380.21861350.20112551390100
3.5638-3.69110.31681390.208112331372100
3.6911-3.83880.2661320.201512641396100
3.8388-4.01350.2041220.200212671389100
4.0135-4.22490.23641590.18411971356100
4.2249-4.48950.21311300.17812531383100
4.4895-4.83580.21071440.193212231367100
4.8358-5.32190.2211520.186312321384100
5.3219-6.09070.23441480.206312251373100
6.0907-7.66870.25011300.24612581388100
7.6687-48.34510.22621390.19461230136999

+
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