[English] 日本語
Yorodumi
- PDB-4ia8: Crystal Structure of a Y37A mutant of the Restriction-Modificatio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ia8
TitleCrystal Structure of a Y37A mutant of the Restriction-Modification Controller Protein C.Esp1396I
ComponentsRegulatory protein
KeywordsTRANSCRIPTION / Restriction-modification / helix-turn-helix / transcriptional regulator / DNA
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
: / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesEnterobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsMartin, R.N.A. / McGeehan, J.E. / Kneale, G.G.
Citation
Journal: Plos One / Year: 2014
Title: Structural and Mutagenic Analysis of the RM Controller Protein C.Esp1396I.
Authors: Martin, R.N. / McGeehan, J.E. / Kneale, G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the restriction-modification controller protein C.Esp1396I.
Authors: Ball, N. / Streeter, S.D. / Kneale, G.G. / McGeehan, J.E.
#2: Journal: Nucleic Acids Res. / Year: 2012
Title: Recognition of dual symmetry by the controller protein C.Esp1396I based on the structure of the transcriptional activation complex.
Authors: McGeehan, J.E. / Ball, N.J. / Streeter, S.D. / Thresh, S.J. / Kneale, G.G.
#3: Journal: Nucleic Acids Res. / Year: 2012
Title: The structural basis of differential DNA sequence recognition by restriction-modification controller proteins.
Authors: Ball, N.J. / McGeehan, J.E. / Streeter, S.D. / Thresh, S.J. / Kneale, G.G.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the restriction-modification controller protein C.Esp1396I.
Authors: Ball, N. / Streeter, S.D. / Kneale, G.G. / McGeehan, J.E.
History
DepositionDec 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Regulatory protein
B: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9543
Polymers18,8582
Non-polymers961
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-28 kcal/mol
Surface area8240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.260, 34.280, 41.120
Angle α, β, γ (deg.)104.440, 108.920, 97.420
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Regulatory protein


Mass: 9429.078 Da / Num. of mol.: 2 / Mutation: A37W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter sp. (bacteria) / Strain: RFL1396 / Gene: esp1396IC / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8GGH0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2 M lithium sulfate, 0.1 M sodium acetate, 50 % v/v PEG 400, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917285 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 22, 2011
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917285 Å / Relative weight: 1
ReflectionResolution: 1.85→31.55 Å / Num. all: 19685 / Num. obs: 13243 / % possible obs: 75 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 5.8
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique all% possible all
1.85-1.891.91.5292773379.1
9.06-31.552.11447311595.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.27 Å31.55 Å
Translation4.27 Å31.55 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.1.26data scaling
PHASER2.5.1phasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3G5G

3g5g


Resolution: 1.85→31.55 Å / Occupancy max: 1 / Occupancy min: 0.17 / FOM work R set: 0.885 / SU ML: 0.14 / σ(F): 5.63 / Phase error: 18.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2202 676 5.29 %
Rwork0.1747 --
obs0.1769 12775 89.65 %
all-19685 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.26 Å2 / Biso mean: 29.4732 Å2 / Biso min: 9.82 Å2
Refinement stepCycle: LAST / Resolution: 1.85→31.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 5 44 1293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181298
X-RAY DIFFRACTIONf_angle_d1.7321744
X-RAY DIFFRACTIONf_chiral_restr0.127210
X-RAY DIFFRACTIONf_plane_restr0.008214
X-RAY DIFFRACTIONf_dihedral_angle_d15.347524
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8501-1.99290.1761520.11822489264192
1.9929-2.19340.19461390.12772463260291
2.1934-2.51070.21081490.15922292244186
2.5107-3.16280.23141150.19642489260491
3.1628-32.3180.23541210.19032366248787
Refinement TLS params.Method: refined / Origin x: 11.4798 Å / Origin y: 3.8852 Å / Origin z: 28.8809 Å
111213212223313233
T0.1263 Å20.023 Å20.0238 Å2-0.129 Å20.0319 Å2--0.1152 Å2
L1.677 °21.1874 °21.4791 °2-2.2313 °21.8303 °2--2.1654 °2
S-0.0364 Å °0.0428 Å °0.0934 Å °0.0326 Å °-0.0229 Å °0.0993 Å °-0.0581 Å °-0.0397 Å °0.0536 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 79
2X-RAY DIFFRACTION1allB3 - 79
3X-RAY DIFFRACTION1allB1 - 101
4X-RAY DIFFRACTION1allB1 - 224

+
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