[English] 日本語
Yorodumi
- PDB-4pbb: The 5-Hydroxymethylcytosine-Specific Restriction Enzyme AbaSI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pbb
TitleThe 5-Hydroxymethylcytosine-Specific Restriction Enzyme AbaSI
ComponentsUncharacterized protein AbaSI
KeywordsDNA BINDING PROTEIN / Hydroxymethylcytosine-dependent restriction enzyme / hydrolase / VSR endonuclease-like / SRA domain-like / Epigenetic sequencing tool
Function / homologySET and RING associated domain / : / SET and RING associated domain / Restriction endonuclease PvuRts1 I-like, N-terminal / Uncharacterized protein
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.46 Å
AuthorsHorton, J.R. / Cheng, X.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA.
Authors: Horton, J.R. / Borgaro, J.G. / Griggs, R.M. / Quimby, A. / Guan, S. / Zhang, X. / Wilson, G.G. / Zheng, Y. / Zhu, Z. / Cheng, X.
History
DepositionApr 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Mar 27, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein AbaSI
B: Uncharacterized protein AbaSI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8287
Polymers75,3482
Non-polymers4805
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-77 kcal/mol
Surface area30110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.428, 92.352, 180.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Uncharacterized protein AbaSI


Mass: 37673.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: SDF / Gene: ABSDF3356 / Production host: Escherichia coli (E. coli) / Variant (production host): BL21(DE3) / References: UniProt: B0VN39
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 67.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: ammonium sulfate, HEPES / PH range: 6.4 - 7.4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.45→32.21 Å / Num. obs: 15301 / % possible obs: 100 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.166 / Net I/σ(I): 9.8
Reflection shellResolution: 3.45→3.61 Å / Redundancy: 5 % / % possible all: 100

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1593) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: low resolution Se-SAD structures

Resolution: 3.46→32.206 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2795 752 5 %
Rwork0.2405 --
obs0.2426 15029 97.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.46→32.206 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5193 0 25 0 5218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035321
X-RAY DIFFRACTIONf_angle_d0.837184
X-RAY DIFFRACTIONf_dihedral_angle_d12.2382016
X-RAY DIFFRACTIONf_chiral_restr0.034781
X-RAY DIFFRACTIONf_plane_restr0.003912
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4597-3.72650.3891440.3582746X-RAY DIFFRACTION96
3.7265-4.10080.36191480.30892788X-RAY DIFFRACTION97
4.1008-4.69270.30841460.24212795X-RAY DIFFRACTION97
4.6927-5.90630.27581530.22922890X-RAY DIFFRACTION99
5.9063-32.20710.21521610.19543058X-RAY DIFFRACTION100
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)
13.72710.66231.42885.9-1.82198.36650.1949-0.4805-0.01250.49710.1673-0.07330.0207-0.3371-0.37290.65010.0320.03920.6406-0.00810.62613.138153.8947-65.6717
23.40081.3075-2.24622.1767-2.94766.8514-0.01470.0377-0.2282-0.1870.1217-0.03620.5603-0.3137-0.13240.64930.099-0.07550.63570.00090.76977.212757.9503-92.4562
33.6491-0.04371.26964.5322-0.13668.8616-0.06520.2923-0.5304-0.64870.2044-0.12071.04840.1825-0.1050.9748-0.01140.00740.66340.0780.8239.033230.8638-54.8418
47.3885-1.70772.50975.6394-1.88218.9439-0.18890.5876-0.0044-0.08380.1685-0.30720.07210.4784-0.00260.63590.02910.05580.5664-0.01440.632320.031930.4658-28.8417
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:151)
2X-RAY DIFFRACTION2(chain A and resid 152:318)
3X-RAY DIFFRACTION3(chain B and resid 5:173)
4X-RAY DIFFRACTION4(chain B and resid 174:317)

+
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