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- PDB-4x4d: RADIATION DAMAGE TO THE NUCLEOPROTEIN COMPLEX C.Esp1396I: DOSE (D... -

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Basic information

Entry
Database: PDB / ID: 4x4d
TitleRADIATION DAMAGE TO THE NUCLEOPROTEIN COMPLEX C.Esp1396I: DOSE (DWD) 10.3 MGy
Components
  • (35-MER DNA) x 2
  • Regulatory protein
KeywordsGENE REGULATION / protein-DNA complex / radiation damage
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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,6166
Polymers59,6166
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13080 Å2
ΔGint-73 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.400, 104.400, 139.160
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.

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Components

#1: Protein
Regulatory protein / 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)

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: MES, MPD, MgCl2

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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→69.6 Å / Num. obs: 21198 / % possible obs: 99.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 63 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.023 / Net I/σ(I): 22.4 / Num. measured all: 128743 / Scaling rejects: 166
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.8-2.956.20.454.21922931000.9120.197100
8.85-69.65.50.02151.437096760.9890.01196.2

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3clc


Resolution: 2.8→19.038 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 33.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2824 1075 5.09 %5% random selection
Rwork0.2346 20043 --
obs0.2371 21118 99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.21 Å2 / Biso mean: 62.959 Å2 / Biso min: 27.65 Å2
Refinement stepCycle: final / Resolution: 2.8→19.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 1429 0 0 3925
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 (%)
2.8001-2.92710.41011380.383525062644100
2.9271-3.08080.41411590.339824652624100
3.0808-3.2730.36041080.301425452653100
3.273-3.52420.31691270.282524872614100
3.5242-3.87610.38371320.266925232655100
3.8761-4.43090.29081510.220324652616100
4.4309-5.55930.26251320.196425282660100
5.5593-19.03880.14281280.1632524265299

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