[English] 日本語
Yorodumi
- PDB-4beb: MUTANT (K220E) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION EN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4beb
TitleMUTANT (K220E) OF THE HSDR SUBUNIT OF THE ECOR124I RESTRICTION ENZYME IN COMPLEX WITH ATP
ComponentsTYPE I RESTRICTION ENZYME HSDR
KeywordsHYDROLASE / DNA MODIFICATION
Function / homology
Function and homology information


type I site-specific deoxyribonuclease / type I site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / ATP binding
Similarity search - Function
tt1808, chain A - #50 / Actin; Chain A, domain 4 - #50 / tt1808, chain A / Restriction endonuclease, type I, HsdR, N-terminal / Type I restriction enzyme R protein, C-terminal / SWI2/SNF2 ATPase / : / : / Type I restriction enzyme R protein N terminus (HSDR_N) / Type I restriction and modification enzyme - subunit R C terminal ...tt1808, chain A - #50 / Actin; Chain A, domain 4 - #50 / tt1808, chain A / Restriction endonuclease, type I, HsdR, N-terminal / Type I restriction enzyme R protein, C-terminal / SWI2/SNF2 ATPase / : / : / Type I restriction enzyme R protein N terminus (HSDR_N) / Type I restriction and modification enzyme - subunit R C terminal / SWI2/SNF2 ATPase / Type I restriction enzyme subunit R domain 3 / Restriction endonuclease, type I, HsdR / Actin; Chain A, domain 4 / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Complex / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Type I restriction enzyme EcoR124I/EcoR124II endonuclease subunit / Type I restriction enzyme EcoR124I/EcoR124II endonuclease subunit
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.989 Å
AuthorsCsefalvay, E. / Lapkouski, M. / Guzanova, A. / Csefalvay, L. / Baikova, T. / Shevelev, I. / Janscak, P. / Smatanova, I.K. / Panjikar, S. / Carey, J. ...Csefalvay, E. / Lapkouski, M. / Guzanova, A. / Csefalvay, L. / Baikova, T. / Shevelev, I. / Janscak, P. / Smatanova, I.K. / Panjikar, S. / Carey, J. / Weiserova, M. / Ettrich, R.
CitationJournal: Plos One / Year: 2015
Title: Functional Coupling of Duplex Translocation to DNA Cleavage in a Type I Restriction Enzyme.
Authors: Csefalvay, E. / Lapkouski, M. / Guzanova, A. / Csefalvay, L. / Baikova, T. / Shevelev, I. / Bialevich, V. / Shamayeva, K. / Janscak, P. / Kuta Smatanova, I. / Panjikar, S. / Carey, J. / ...Authors: Csefalvay, E. / Lapkouski, M. / Guzanova, A. / Csefalvay, L. / Baikova, T. / Shevelev, I. / Bialevich, V. / Shamayeva, K. / Janscak, P. / Kuta Smatanova, I. / Panjikar, S. / Carey, J. / Weiserova, M. / Ettrich, R.
History
DepositionMar 7, 2013Deposition site: PDBE / Processing site: PDBE
SupersessionMar 26, 2014ID: 2Y3T
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: TYPE I RESTRICTION ENZYME HSDR
B: TYPE I RESTRICTION ENZYME HSDR
C: TYPE I RESTRICTION ENZYME HSDR
D: TYPE I RESTRICTION ENZYME HSDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)483,24112
Polymers481,1154
Non-polymers2,1268
Water00
1
A: TYPE I RESTRICTION ENZYME HSDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,8103
Polymers120,2791
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TYPE I RESTRICTION ENZYME HSDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,8103
Polymers120,2791
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TYPE I RESTRICTION ENZYME HSDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,8103
Polymers120,2791
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TYPE I RESTRICTION ENZYME HSDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,8103
Polymers120,2791
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.112, 123.112, 160.110
Angle α, β, γ (deg.)90.00, 111.48, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1, 0.002365, 0.006688), (-0.002352, 1, -0.00205), (-0.006692, 0.002035, 1)-29.84, 19.04, 74.85
2given(-1, -0.002003, -0.000989), (0.00199, -0.9999, 0.01292), (-0.001015, 0.01291, 0.9999)-24.28, 18.38, 74.83
3given(-1, -0.00354, 0.002323), (0.003588, -0.9998, 0.02071), (0.002249, 0.02072, 0.9998)4.826, -1.047, 0.065

-
Components

#1: Protein
TYPE I RESTRICTION ENZYME HSDR


Mass: 120278.797 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q304R3, UniProt: P10486*PLUS, type I site-specific deoxyribonuclease
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 6UL PROTEIN MIXED WITH 0.8UL OF 2M NH4F AND 2UL WELL SOLUTION OF 22% W/V PEG4K, 0.1M MES PH 5.7. 20C, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815
DetectorType: MARRESEARCH MX-555 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 2.989→20 Å / Num. obs: 92081 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 41.12 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.7
Reflection shellResolution: 2.989→3.17 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.7 / % possible all: 96.2

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPIN AUTO-RICKSHAW PACKAGEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W00

2w00


Resolution: 2.989→19.885 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 35.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2965 968 1.1 %
Rwork0.255 --
obs0.2555 91171 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.14 Å2
Refinement stepCycle: LAST / Resolution: 2.989→19.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27241 0 128 0 27369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00427899
X-RAY DIFFRACTIONf_angle_d0.99937673
X-RAY DIFFRACTIONf_dihedral_angle_d13.58510343
X-RAY DIFFRACTIONf_chiral_restr0.074129
X-RAY DIFFRACTIONf_plane_restr0.0044869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9895-3.14650.34721190.297612084X-RAY DIFFRACTION92
3.1465-3.34280.37391500.289712829X-RAY DIFFRACTION99
3.3428-3.59950.31491410.261212907X-RAY DIFFRACTION99
3.5995-3.95910.28991470.246913017X-RAY DIFFRACTION100
3.9591-4.52610.28061570.232613049X-RAY DIFFRACTION100
4.5261-5.68030.25321340.238413124X-RAY DIFFRACTION100
5.6803-19.88520.28351200.257513193X-RAY DIFFRACTION99

+
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