[English] 日本語
Yorodumi
- PDB-4x4b: RADIATION DAMAGE TO THE NUCLEOPROTEIN COMPLEX C.Esp1396I: DOSE (D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4x4b
TitleRADIATION DAMAGE TO THE NUCLEOPROTEIN COMPLEX C.Esp1396I: DOSE (DWD) 2.1 MGy
Components
  • (35-MER DNA) x 2
  • Regulatory proteinRegulation of gene expression
KeywordsGENE REGULATION / protein-DNA complex / radiation damage
Function / homology
Function and homology information


Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / 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) / Regulatory protein
Similarity search - Component
Biological speciesEnterobacter sp. RFL1396 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsBury, C.S. / McGeehan, J.E. / Garman, E.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
Citation
Journal: J.Synchrotron Radiat. / Year: 2015
Title: Radiation damage to nucleoprotein complexes in macromolecular crystallography.
Authors: Bury, C. / Garman, E.F. / Ginn, H.M. / Ravelli, R.B. / Carmichael, I. / Kneale, G. / McGeehan, J.E.
#1: Journal: Nucleic Acids Res. / Year: 2008
Title: Structural analysis of the genetic switch that regulates the expression of restriction-modification genes
Authors: McGeehan, J.E. / Streeter, S.D. / Thresh, S.J. / Ball, N. / Ravelli, R.B.G. / Kneale, G.G.
History
DepositionDec 2, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Regulatory protein
B: Regulatory protein
C: Regulatory protein
D: Regulatory protein
E: 35-MER DNA
F: 35-MER DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6648
Polymers59,6166
Non-polymers492
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13360 Å2
ΔGint-93 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.310, 104.310, 139.130
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
12chain E
22chain F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULYSLYSchain AAA2 - 775 - 80
21GLUGLUHISHISchain BBB2 - 785 - 81
31GLUGLUHISHISchain CCC2 - 785 - 81
41GLUGLULYSLYSchain DDD2 - 775 - 80
12DADADTDTchain EEE1 - 351 - 35
22DADADTDTchain FFF1 - 351 - 35

NCS ensembles :
ID
1
2
Detailsbiological unit is the same as asym.

-
Components

#1: Protein
Regulatory protein / Regulation of gene expression / Controller protein


Mass: 9521.175 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter sp. RFL1396 (bacteria) / Gene: esp1396IC / Plasmid: pET23 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD / References: UniProt: Q8GGH0
#2: DNA chain 35-MER DNA


Mass: 10791.966 Da / Num. of mol.: 1 / Fragment: Operator DNA / Source method: obtained synthetically / Details: Chemically synthesised DNA / Source: (synth.) synthetic construct (others)
#3: DNA chain 35-MER DNA


Mass: 10738.960 Da / Num. of mol.: 1 / Fragment: Operator DNA / Source method: obtained synthetically / Details: Chemically synthesised DNA / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Fragment: MAGNESIUM ION / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.67 Å3/Da / Density % sol: 66.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: MES, MPD, MgCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9322 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 29, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9322 Å / Relative weight: 1
ReflectionResolution: 2.8→69.59 Å / Num. obs: 21172 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 55.92 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.022 / Net I/σ(I): 24 / Num. measured all: 128219 / Scaling rejects: 175
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.8-2.996.20.335.52375338400.950.145100
7.92-69.595.70.02155.352959350.990.0196.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXrefinement
MOSFLMdata reduction
Aimless0.2.8data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CLC

3clc


Resolution: 2.8→19.028 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Phase error: 30.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2616 1072 5.09 %5% random selection
Rwork0.2045 19996 --
obs0.2075 21068 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.91 Å2 / Biso mean: 62.1817 Å2 / Biso min: 20.75 Å2
Refinement stepCycle: final / Resolution: 2.8→19.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 1429 2 5 3932
Biso mean--39.89 30.38 -
Num. residues----376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114120
X-RAY DIFFRACTIONf_angle_d1.3385823
X-RAY DIFFRACTIONf_chiral_restr0.062680
X-RAY DIFFRACTIONf_plane_restr0.005474
X-RAY DIFFRACTIONf_dihedral_angle_d25.2571686
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1496X-RAY DIFFRACTION17.228TORSIONAL
12B1496X-RAY DIFFRACTION17.228TORSIONAL
13C1496X-RAY DIFFRACTION17.228TORSIONAL
14D1496X-RAY DIFFRACTION17.228TORSIONAL
21E498X-RAY DIFFRACTION17.228TORSIONAL
22F498X-RAY DIFFRACTION17.228TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.92710.41681400.338924882628100
2.9271-3.08080.36551570.296924682625100
3.0808-3.27290.31691060.252825292635100
3.2729-3.52410.25291250.235925012626100
3.5241-3.8760.33651320.216625042636100
3.876-4.43070.27031530.18524612614100
4.4307-5.55910.23231300.166425282658100
5.5591-19.02810.15221290.15612517264699
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)
10.0927-0.09320.06780.2011-0.10110.0731-0.38270.2067-0.18590.1380.3834-0.52210.03540.0233-0.0589-0.2638-0.3077-0.11680.7102-0.23060.3745-16.249623.0336-5.5475
20.1067-0.04350.10480.11130.0210.182-0.070.1766-0.0571-0.05060.35010.3765-0.18320.29630.27250.147-0.09980.0010.5508-0.00270.3411-34.254223.2155-16.344
30.06990.09840.07990.25590.02670.1228-0.059-0.2149-0.03920.03990.2123-0.3851-0.1222-0.15540.14510.1780.10450.00430.49850.02480.3622-69.980723.231-6.9145
40.07780.07090.06290.20110.1030.0648-0.2214-0.1589-0.3348-0.23020.24850.3808-0.0534-0.0008-0.0491-0.10890.2821-0.14770.75180.23980.3464-88.070223.1106-17.6196
50.87110.0222-0.23340.5296-0.37950.33350.1963-0.05490.3663-0.08490.2918-0.1353-0.4055-0.09640.62290.23910.0760.00050.8721-0.03530.467-52.147527.1457-11.9055
60.8978-0.0642-0.29020.530.33410.42620.2650.04810.31290.0890.21080.0896-0.37110.14840.57290.2049-0.06870.04310.81610.03690.4742-52.112727.1443-11.2024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 2:77)A2 - 77
2X-RAY DIFFRACTION2(chain B and resseq 2:78)B2 - 78
3X-RAY DIFFRACTION3(chain C and resseq 2:78)C2 - 78
4X-RAY DIFFRACTION4(chain D and resseq 2:77)D2 - 77
5X-RAY DIFFRACTION5(chain E and resseq 1:36)E1 - 36
6X-RAY DIFFRACTION6(chain F and resseq 1:36)F1 - 36

+
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