[English] 日本語
Yorodumi
- PDB-4i6r: High Resolution Crystal Structure of the Wild-Type Restriction-Mo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i6r
TitleHigh Resolution Crystal Structure of the Wild-Type Restriction-Modification Controller Protein C.Esp1396I (Triclinic form)
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: 1.38 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
DepositionNov 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 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)19,79110
Polymers19,0422
Non-polymers7498
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-53 kcal/mol
Surface area8420 Å2
MethodPISA
2
A: Regulatory protein
hetero molecules

B: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,79110
Polymers19,0422
Non-polymers7498
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_566x,y+1,z+11
Buried area1830 Å2
ΔGint-47 kcal/mol
Surface area9920 Å2
MethodPISA
3
A: Regulatory protein
hetero molecules

B: Regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,79110
Polymers19,0422
Non-polymers7498
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_666x+1,y+1,z+11
Buried area1940 Å2
ΔGint-48 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.760, 34.780, 41.860
Angle α, β, γ (deg.)110.470, 105.600, 96.000
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Regulatory protein


Mass: 9521.175 Da / Num. of mol.: 2
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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M MMT buffer, 100 mM Sodium Sulphate, 25% PEG 1500, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 15, 2012
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.38→37.049 Å / Num. all: 112030 / Num. obs: 31070 / % possible obs: 83.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.38-1.413.80.3745986157083.8
7.31-25.793.90.04234.990923496.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.38 Å25.79 Å
Translation1.38 Å25.79 Å

-
Processing

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

3g5g


Resolution: 1.38→25.79 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.1887 / WRfactor Rwork: 0.1558 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.889 / SU B: 1.659 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0561 / SU Rfree: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1815 1470 5 %RANDOM
Rwork0.1489 ---
obs0.1505 29524 83.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.18 Å2 / Biso mean: 15.78 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.04 Å20.02 Å2
2---0.02 Å2-0.02 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.38→25.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 45 78 1381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0191359
X-RAY DIFFRACTIONr_bond_other_d0.0020.021400
X-RAY DIFFRACTIONr_angle_refined_deg2.6962.0291821
X-RAY DIFFRACTIONr_angle_other_deg1.10633250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0325172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.56524.44454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51715300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.762158
X-RAY DIFFRACTIONr_chiral_restr0.1770.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021426
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02274
LS refinement shellResolution: 1.382→1.418 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 98 -
Rwork0.179 2049 -
all-2147 -
obs--83.06 %
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)
10.0837-0.2042-0.07561.14480.57020.8208-0.0252-0.0255-0.03070.06180.02450.03890.00930.03780.00070.1032-0.0513-0.03160.04850.03650.03142.706-6.786-21.369
21.50520.0240.68270.1440.19860.68330.02330.05980.0419-0.0242-0.0197-0.01360.03320.0083-0.00370.0989-0.0509-0.03630.05910.03760.0246-5.188-15.672-36.877
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 79
2X-RAY DIFFRACTION1A101 - 104
3X-RAY DIFFRACTION1A201 - 240
4X-RAY DIFFRACTION2B3 - 79
5X-RAY DIFFRACTION2B101 - 104
6X-RAY DIFFRACTION2B201 - 238

+
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