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- PDB-5jvf: Crystal Structure of Apo-FleN -

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Basic information

Entry
Database: PDB / ID: 5jvf
TitleCrystal Structure of Apo-FleN
ComponentsSite-determining protein
KeywordsTRANSCRIPTION / FleN / Antiactivator / Pseudomonas
Function / homology
Function and homology information


cytoplasmic side of plasma membrane / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
Flagellum site-determining protein FlhG / Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 / NUBPL iron-transfer P-loop NTPase / ATP binding protein MinD/FleN / : / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
IODIDE ION / Antiactivator FleN
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.66 Å
AuthorsJain, D. / Chanchal / Banerjee, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology India
CitationJournal: Structure / Year: 2017
Title: ATP-Induced Structural Remodeling in the Antiactivator FleN Enables Formation of the Functional Dimeric Form
Authors: Chanchal / Banerjee, P. / Jain, D.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Site-determining protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,50218
Polymers30,4841
Non-polymers2,01817
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-1 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.250, 66.250, 112.870
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
11A-301-

IOD

21A-571-

HOH

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Components

#1: Protein Site-determining protein


Mass: 30484.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: fleN / Production host: Escherichia coli (E. coli) / References: UniProt: G3XD64
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.2M Ammonium iodide, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.66→28.69 Å / Num. obs: 65124 / % possible obs: 99.6 % / Redundancy: 7.3 % / Net I/σ(I): 17.6
Reflection shellResolution: 1.66→1.75 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.66→25.573 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 23.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2171 3305 5.07 %
Rwork0.1886 --
obs0.1901 65124 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.66→25.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1997 0 37 227 2261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072076
X-RAY DIFFRACTIONf_angle_d1.0952818
X-RAY DIFFRACTIONf_dihedral_angle_d14.346773
X-RAY DIFFRACTIONf_chiral_restr0.045339
X-RAY DIFFRACTIONf_plane_restr0.005361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.68370.29641580.27052512X-RAY DIFFRACTION100
1.6837-1.70890.2581510.25822589X-RAY DIFFRACTION100
1.7089-1.73560.311360.25212589X-RAY DIFFRACTION100
1.7356-1.7640.26831390.24832558X-RAY DIFFRACTION100
1.764-1.79440.34071240.23862684X-RAY DIFFRACTION100
1.7944-1.8270.27091480.23272526X-RAY DIFFRACTION100
1.827-1.86220.28781360.22122582X-RAY DIFFRACTION100
1.8622-1.90020.23351510.21932589X-RAY DIFFRACTION100
1.9002-1.94150.27521120.20712613X-RAY DIFFRACTION100
1.9415-1.98660.29951310.2122613X-RAY DIFFRACTION100
1.9866-2.03630.24061160.19152558X-RAY DIFFRACTION100
2.0363-2.09130.25761230.20852638X-RAY DIFFRACTION100
2.0913-2.15280.24211200.19672603X-RAY DIFFRACTION100
2.1528-2.22230.25291440.20762596X-RAY DIFFRACTION100
2.2223-2.30160.26471340.20012575X-RAY DIFFRACTION100
2.3016-2.39370.24831230.20212591X-RAY DIFFRACTION100
2.3937-2.50260.20281520.19842559X-RAY DIFFRACTION100
2.5026-2.63440.22821490.2022610X-RAY DIFFRACTION100
2.6344-2.79930.26531260.20132582X-RAY DIFFRACTION100
2.7993-3.01510.23331590.18522591X-RAY DIFFRACTION100
3.0151-3.31790.18741340.18282599X-RAY DIFFRACTION100
3.3179-3.79670.14421750.15092521X-RAY DIFFRACTION100
3.7967-4.77830.18311290.14762594X-RAY DIFFRACTION99
4.7783-25.57580.21931350.19422347X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 29.774 Å / Origin y: 1.909 Å / Origin z: 50.341 Å
111213212223313233
T0.21 Å2-0.0295 Å20.013 Å2-0.1703 Å20.026 Å2--0.2169 Å2
L0.6244 °20.194 °20.059 °2-1.3096 °2-0.1345 °2--1.333 °2
S0.019 Å °0.1064 Å °0.0946 Å °-0.192 Å °0.118 Å °0.0613 Å °0.045 Å °-0.0675 Å °-0.1433 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 8 through 273 )

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