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- PDB-2ef8: Crystal structure of C.EcoT38IS -

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Basic information

Entry
Database: PDB / ID: 2ef8
TitleCrystal structure of C.EcoT38IS
ComponentsPutative transcription factor
KeywordsTRANSCRIPTION REGULATOR / helix-turn-helix / DNA binding protein
Function / homology
Function and homology information


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
Putative transcription factor
Similarity search - Component
Biological speciesEnterobacteria phage P2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.95 Å
AuthorsKawanishi, Y. / Mikami, B. / Kita, K.
CitationJournal: To be published
Title: Crystal structure of C.EcoT38IS
Authors: Kawanishi, Y. / Mikami, B. / Kita, K.
History
DepositionFeb 21, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative transcription factor
B: Putative transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5133
Polymers19,4172
Non-polymers961
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.420, 56.952, 61.742
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative transcription factor / C.EcoT38IS


Mass: 9708.261 Da / Num. of mol.: 2 / Fragment: subunit A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P2 (virus) / Genus: P2-like viruses / Strain: TH38 / Gene: ecoT38IC / Plasmid: pBSCEcoT38IS-Hisx6 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q83VS9
#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.: 158 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.0M Ammonium Sulfate, 0.1M Sodium Acetate trihydrate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 13, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→27.1 Å / Num. all: 13995 / Num. obs: 13953 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 23.1
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 9.5 / Num. unique all: 1381 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 1.95→14.92 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2712930.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1370 9.9 %RANDOM
Rwork0.202 ---
obs0.202 13883 99.5 %-
all-13953 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.6166 Å2 / ksol: 0.404147 e/Å3
Displacement parametersBiso mean: 24.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2---1.01 Å20 Å2
3---0.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→14.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 5 158 1558
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d18.6
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.192
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.292.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 212 9.3 %
Rwork0.205 2059 -
obs-1370 100 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep10.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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