[English] 日本語
Yorodumi
- PDB-4oc8: DNA modification-dependent restriction endonuclease AspBHI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oc8
TitleDNA modification-dependent restriction endonuclease AspBHI
Componentsrestriction endonuclease AspBHI
KeywordsHYDROLASE / DNA Cleavage / DNA Restriction Enzymes / DNA-Binding Proteins / Tetramerization / Models / Molecular / Azoarcus / Protein Multimerization / Protein Structure / Tertiary
Function / homology
Function and homology information


DNA restriction-modification system / endonuclease activity / DNA binding
Similarity search - Function
PUA domain-like - #20 / Restriction endonuclease AspBHI, N-terminal / Restriction endonuclease AspBHI N-terminal / Restriction endonuclease type IV, Mrr / Restriction endonuclease / PUA domain-like / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / Roll / 3-Layer(aba) Sandwich ...PUA domain-like - #20 / Restriction endonuclease AspBHI, N-terminal / Restriction endonuclease AspBHI N-terminal / Restriction endonuclease type IV, Mrr / Restriction endonuclease / PUA domain-like / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Uncharacterized protein
Similarity search - Component
Biological speciesAzoarcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.884 Å
AuthorsHorton, J.R.
CitationJournal: Sci Rep / Year: 2014
Title: Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI.
Authors: Horton, J.R. / Nugent, R.L. / Li, A. / Mabuchi, M.Y. / Fomenkov, A. / Cohen-Karni, D. / Griggs, R.M. / Zhang, X. / Wilson, G.G. / Zheng, Y. / Xu, S.Y. / Cheng, X.
History
DepositionJan 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: restriction endonuclease AspBHI
B: restriction endonuclease AspBHI
C: restriction endonuclease AspBHI
D: restriction endonuclease AspBHI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,02212
Polymers171,2624
Non-polymers7608
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12090 Å2
ΔGint-85 kcal/mol
Surface area49550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.092, 195.092, 81.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

-
Components

#1: Protein
restriction endonuclease AspBHI


Mass: 42815.582 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azoarcus sp. (bacteria) / Strain: BH72 / Gene: azo0355 / Production host: Escherichia coli (E. coli) / References: UniProt: A1K2B7
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 12% polyethylene glycol 3350, 0.5 M K2HPO4/Na2HPO4, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.06296 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 19, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06296 Å / Relative weight: 1
ReflectionResolution: 2.89→30.74 Å / Num. all: 40080 / Num. obs: 40065 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 64.14 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 19.7
Reflection shellResolution: 2.89→2.99 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 3 / % possible all: 100

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX(phenix.refine: 1.8_1069)model building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8_1069phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.884→30.739 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 26.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 2011 5.03 %
Rwork0.1971 --
obs0.199 39996 99.79 %
all-39996 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.02 Å2
Refinement stepCycle: LAST / Resolution: 2.884→30.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9402 0 40 53 9495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049694
X-RAY DIFFRACTIONf_angle_d0.86913228
X-RAY DIFFRACTIONf_dihedral_angle_d12.7133506
X-RAY DIFFRACTIONf_chiral_restr0.061465
X-RAY DIFFRACTIONf_plane_restr0.0031726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8839-2.9560.36811030.27242707X-RAY DIFFRACTION99
2.956-3.03580.34482060.2572619X-RAY DIFFRACTION100
3.0358-3.12510.27921010.24482753X-RAY DIFFRACTION100
3.1251-3.22580.28762040.23612633X-RAY DIFFRACTION100
3.2258-3.3410.27541020.22482743X-RAY DIFFRACTION100
3.341-3.47460.27921000.20872745X-RAY DIFFRACTION100
3.4746-3.63250.26312020.19852649X-RAY DIFFRACTION100
3.6325-3.82370.24881010.19742736X-RAY DIFFRACTION100
3.8237-4.06280.23141960.18332683X-RAY DIFFRACTION100
4.0628-4.37560.1603970.16512731X-RAY DIFFRACTION100
4.3756-4.81450.21871620.15822709X-RAY DIFFRACTION100
4.8145-5.50770.20861460.16762725X-RAY DIFFRACTION100
5.5077-6.9260.2441020.19762788X-RAY DIFFRACTION100
6.926-30.74030.19721890.2132764X-RAY DIFFRACTION100

+
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