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- PDB-1g8e: CRYSTAL STRUCTURE OF FLHD FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1g8e
TitleCRYSTAL STRUCTURE OF FLHD FROM ESCHERICHIA COLI
ComponentsFLAGELLAR TRANSCRIPTIONAL ACTIVATOR FLHD
KeywordsTRANSCRIPTION / genetic regulator / DNA binding protein
Function / homology
Function and homology information


positive regulation of bacterial-type flagellum assembly / bacterial-type flagellum assembly / transcription regulator complex / DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Flagellar transcriptional activator fold / Flagellar transcriptional activator FlhD / Flagellar transcriptional activator FlhD / Flagellar transcriptional activator FlhD superfamily / Flagellar transcriptional activator (FlhD) / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Flagellar transcriptional regulator FlhD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsCampos, A. / Zhang, R.G. / Alkire, R.W. / Matsumura, P. / Westbrook, E.M.
CitationJournal: Mol.Microbiol. / Year: 2001
Title: Crystal structure of the global regulator FlhD from Escherichia coli at 1.8 A resolution.
Authors: Campos, A. / Zhang, R.G. / Alkire, R.W. / Matsumura, P. / Westbrook, E.M.
History
DepositionNov 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Remark 999SEQUENCE Mass Spectrometry experiments (Soutouroina et al, 1999, J Bacteriol 181: 7500-7508) has ...SEQUENCE Mass Spectrometry experiments (Soutouroina et al, 1999, J Bacteriol 181: 7500-7508) has demonstrated that FlhD from Escherichia coli, contains 116 residues, not 119 as in the sequence database reference. The first putative start codon is not the correct one and the three first residues do not exist.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FLAGELLAR TRANSCRIPTIONAL ACTIVATOR FLHD
B: FLAGELLAR TRANSCRIPTIONAL ACTIVATOR FLHD


Theoretical massNumber of molelcules
Total (without water)26,6672
Polymers26,6672
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-36 kcal/mol
Surface area9570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.717, 88.717, 42.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein FLAGELLAR TRANSCRIPTIONAL ACTIVATOR FLHD


Mass: 13333.386 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PXL25 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P0A8S9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 1.57 Å3/Da / Density % sol: 78.4 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 0.2 M sodium acetate, 30% PEG 5000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
250 mMTris1drop
320-30 %PEG50001reservoir
40.05-0.2 Msodium acetate1reservoir
50.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9464,0.9793,0.9794,1.0332
DetectorType: APS-1 / Detector: CCD / Date: Aug 23, 1998 / Details: sagittal focusing monochromator
RadiationMonochromator: sagittally focused Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.94641
20.97931
30.97941
41.03321
ReflectionResolution: 1.8→10 Å / Num. all: 15124 / Num. obs: 15124 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.33 % / Biso Wilson estimate: 25.02 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 21.4
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.5 / % possible all: 79.6
Reflection
*PLUS
Num. measured all: 50417

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Processing

Software
NameClassification
d*TREKdata scaling
d*TREKdata reduction
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD
Starting model: none

Resolution: 1.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.299 747 random
Rwork0.218 --
all0.218 15124 -
obs0.218 15124 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.531 Å20 Å20 Å2
2---2.531 Å20 Å2
3---5.042 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1418 0 0 117 1535
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d16.8
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.318 70 4.6 %
Rwork0.299 1519 -
obs-1519 79.6 %
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.8
LS refinement shell
*PLUS
Rfactor Rfree: 0.318 / % reflection Rfree: 4.6 % / Rfactor Rwork: 0.299 / Rfactor obs: 0.299

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