[English] 日本語
Yorodumi
- PDB-4jcx: Crystal structure of the Restriction-Modification Controller Prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jcx
TitleCrystal structure of the Restriction-Modification Controller Protein C.Csp231I OL operator complex
Components
  • Csp231I C protein
  • DNA (5'-D(*AP*CP*AP*CP*TP*AP*AP*GP*GP*AP*AP*AP*AP*CP*TP*TP*AP*GP*TP*AP*A)-3')
  • DNA (5'-D(*TP*TP*AP*CP*TP*AP*AP*GP*TP*TP*TP*TP*CP*CP*TP*TP*AP*GP*TP*GP*T)-3')
KeywordsDNA BINDING PROTEIN/DNA / helix-turn-helix / C controller protein / restriction-modification systems / transcriptional regulation / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Helix-turn-helix domain / 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
DNA / DNA (> 10) / Csp231I C protein
Similarity search - Component
Biological speciesCitrobacter sp. RFL231 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShevtsov, M.B. / Streeter, S.D. / Thresh, S.J. / Mcgeehan, J.E. / Kneale, G.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression.
Authors: Shevtsov, M.B. / Streeter, S.D. / Thresh, S.J. / Swiderska, A. / McGeehan, J.E. / Kneale, G.G.
History
DepositionFeb 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Csp231I C protein
B: Csp231I C protein
C: DNA (5'-D(*AP*CP*AP*CP*TP*AP*AP*GP*GP*AP*AP*AP*AP*CP*TP*TP*AP*GP*TP*AP*A)-3')
D: DNA (5'-D(*TP*TP*AP*CP*TP*AP*AP*GP*TP*TP*TP*TP*CP*CP*TP*TP*AP*GP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)35,6424
Polymers35,6424
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-52 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.200, 62.200, 147.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS A PROTEIN DIMER BOUND TO DNA DUPLEX.

-
Components

#1: Protein Csp231I C protein


Mass: 11380.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter sp. RFL231 (bacteria) / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: Q32WH4
#2: DNA chain DNA (5'-D(*AP*CP*AP*CP*TP*AP*AP*GP*GP*AP*AP*AP*AP*CP*TP*TP*AP*GP*TP*AP*A)-3')


Mass: 6472.251 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*TP*AP*CP*TP*AP*AP*GP*TP*TP*TP*TP*CP*CP*TP*TP*AP*GP*TP*GP*T)-3')


Mass: 6409.153 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: Protein was dialysed against the buffer containing 0.1 M NaCl, 50 mM TRIS-HCl, pH 8.2, 1 mM DTT and 1 mM EDTA. Crystallisation conditions: 0.2 M ammonium chloride, 0.1 M MES pH 6.0, 20 % ...Details: Protein was dialysed against the buffer containing 0.1 M NaCl, 50 mM TRIS-HCl, pH 8.2, 1 mM DTT and 1 mM EDTA. Crystallisation conditions: 0.2 M ammonium chloride, 0.1 M MES pH 6.0, 20 % (w/v) PEG6K, protein dimer/DNA molar ratio 1:2, protein concentration 1.2 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.3→50.61 Å / Num. all: 14413 / Num. obs: 14402 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 10.5
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1642 / % possible all: 100

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LFP

3lfp


Resolution: 2.3→50.61 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.887 / SU ML: 0.098 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19647 773 5.4 %RANDOM
Rwork0.17176 ---
obs0.17309 13576 99.9 %-
all-13586 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.251 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1541 855 0 57 2453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0162521
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0361.653572
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.595187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.74623.33378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4715310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.311518
X-RAY DIFFRACTIONr_chiral_restr0.0650.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021603
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 39 -
Rwork0.264 1020 -
obs-1020 99.62 %
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)
13.61720.46-0.34863.44420.92453.46340.1198-0.0067-0.20760.2238-0.02480.25340.2-0.2225-0.0950.0243-0.01360.00450.0428-0.02440.1144-31.114423.10258.2088
25.25960.081-0.23432.65930.26481.51690.04610.09690.115-0.1276-0.00680.45890.0817-0.2375-0.03930.0694-0.0136-0.03420.0525-0.01190.131-25.561611.3394-4.6572
31.7885-0.3097-0.68292.16820.7761.41890.1465-0.07140.4657-0.14570.1461-0.7248-0.16730.2596-0.29260.0832-0.04610.05660.1008-0.04290.3278-9.254827.48290.7811
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 94
2X-RAY DIFFRACTION2B1 - 95
3X-RAY DIFFRACTION3C1 - 21
4X-RAY DIFFRACTION3D1 - 21

+
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