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- PDB-2avu: Structure of the Escherichia coli FlhDC complex, a prokaryotic he... -

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Basic information

Entry
Database: PDB / ID: 2avu
TitleStructure of the Escherichia coli FlhDC complex, a prokaryotic heteromeric regulator of transcription
Components
  • Flagellar transcriptional activator flhC
  • Transcriptional activator flhD
KeywordsTRANSCRIPTION ACTIVATOR / C4-type Zinc finger
Function / homology
Function and homology information


positive regulation of bacterial-type flagellum assembly / bacterial-type flagellum organization / bacterial-type flagellum assembly / transcription regulator complex / DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Flagellar transcriptional activator FlhC / Flagellar transcriptional activator (FlhC) / 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 / Flagellar transcriptional regulator FlhC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsWang, S. / Fleming, R.T. / Westbrook, E.M. / Matsumura, P. / McKay, D.B.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure of the Escherichia coli FlhDC Complex, a Prokaryotic Heteromeric Regulator of Transcription.
Authors: Wang, S. / Fleming, R.T. / Westbrook, E.M. / Matsumura, P. / McKay, D.B.
History
DepositionAug 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Transcriptional activator flhD
B: Transcriptional activator flhD
C: Transcriptional activator flhD
D: Transcriptional activator flhD
E: Flagellar transcriptional activator flhC
F: Flagellar transcriptional activator flhC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6438
Polymers96,5126
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15670 Å2
ΔGint-134 kcal/mol
Surface area29720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.137, 151.137, 114.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsThe biological assembly of the complex is a hexamer which consists of four molecules of FlhD and two molecules of FlhC in the asymmetric unit

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Components

#1: Protein
Transcriptional activator flhD


Mass: 13333.386 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: flhD, flbB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A8S9
#2: Protein Flagellar transcriptional activator flhC


Mass: 21589.084 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: flhC, flaI / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0ABY7
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.967.8
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop7sodium chloride, sodium acetate, ethylene imine polymer, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2982vapor diffusion7.5polyethylene glycol, magnesium acetate, sodium hepes, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.97964
SYNCHROTRONALS 8.2.220.97964
Detector
TypeIDDetector
ADSC QUANTUM 3151CCD
ADSC QUANTUM 3152CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979641
21
ReflectionResolution: 3→50 Å / Num. all: 29628 / Num. obs: 29451 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4.2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 28.3
Reflection shellResolution: 3→3.1 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 4.2 / Num. unique all: 2936 / Rsym value: 0.314 / % possible all: 99.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3→37.79 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 624811.21 / 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
Rfree0.255 1412 4.9 %RANDOM
Rwork0.217 ---
all0.22 29685 --
obs0.217 28854 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.4622 Å2 / ksol: 0.331171 e/Å3
Displacement parametersBiso mean: 77.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å214.35 Å20 Å2
2--1.15 Å20 Å2
3----2.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 3→37.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5314 0 2 0 5316
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 223 5.1 %
Rwork0.351 4185 -
obs-2922 89.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep-kludge.paramprotein.top
X-RAY DIFFRACTION2ion-kludge.param

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