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- PDB-2eby: Crystal structure of a hypothetical protein from E. Coli -

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Basic information

Entry
Database: PDB / ID: 2eby
TitleCrystal structure of a hypothetical protein from E. Coli
ComponentsPutative HTH-type transcriptional regulator ybaQ
KeywordsTRANSCRIPTION / Hypothetical protein / JW0472 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Toxin-antitoxin system, antidote protein, HigA / 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
Uncharacterized HTH-type transcriptional regulator YbaQ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsKarthe, P. / Kumarevel, T.S. / Ebihara, A. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical protein from E. Coli
Authors: Karthe, P. / Kumarevel, T.S. / Ebihara, S. / Kuramitsu, S. / Yokoyama, S.
History
DepositionFeb 9, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Putative HTH-type transcriptional regulator ybaQ
B: Putative HTH-type transcriptional regulator ybaQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7626
Polymers26,3782
Non-polymers3844
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.793, 89.793, 54.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-149-

HOH

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Components

#1: Protein Putative HTH-type transcriptional regulator ybaQ


Mass: 13189.083 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: E.coli cell-free system / Gene: ybaQ / Plasmid: pCR2.1-Topo / References: UniProt: P0A9T6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 9.4
Details: 1.93M Ammonium sulfate, 0.1M CHES, pH 9.4, LIQUID DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97895, 0.97943, 0.9000
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 18, 2006
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978951
20.979431
30.91
ReflectionResolution: 2.25→50 Å / Num. all: 12218 / Num. obs: 12218 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.2 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.077
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.306 / Num. unique all: 1190 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.25→19.93 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1423955.27 / 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
Rfree0.248 614 5 %RANDOM
Rwork0.228 ---
obs0.228 12179 99.9 %-
all-12218 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.6251 Å2 / ksol: 0.365804 e/Å3
Displacement parametersBiso mean: 37.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.3 Å21.39 Å20 Å2
2--4.3 Å20 Å2
3----8.61 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.25→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 20 59 1702
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.322
X-RAY DIFFRACTIONc_scangle_it3.342.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 86 4.4 %
Rwork0.232 1868 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna_rep.param
X-RAY DIFFRACTION4ion.paramion.param

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