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- PDB-5eb1: the YfiB-YfiR complex -

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Basic information

Entry
Database: PDB / ID: 5eb1
Titlethe YfiB-YfiR complex
Components
  • YfiB
  • YfiR
KeywordsMEMBRANE PROTEIN/TRANSCRIPTION / OmpA/Pal-like outer-membrane lipoprotein / periplasmic repressor protein / complex / MEMBRANE PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


cell outer membrane / periplasmic space
Similarity search - Function
YfiR/HmsC-like / YfiR/HmsC-like / OmpA-like domain / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / 60s Ribosomal Protein L30; Chain: A; / Prokaryotic membrane lipoprotein lipid attachment site profile. ...YfiR/HmsC-like / YfiR/HmsC-like / OmpA-like domain / Outer membrane protein, bacterial / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / 60s Ribosomal Protein L30; Chain: A; / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Negative regulator YfiR / Outer-membrane lipoprotein YfiB
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsXu, M. / Yang, X. / Yang, X.-A. / Zhou, L. / Liu, T.-Z. / Fan, Z. / Jiang, T.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation31570768 China
National Natural Science Foundation91419308 China
CitationJournal: Protein Cell / Year: 2016
Title: Structural insights into the regulatory mechanism of the Pseudomonas aeruginosa YfiBNR system
Authors: Xu, M. / Yang, X. / Yang, X.-A. / Zhou, L. / Liu, T.-Z. / Fan, Z. / Jiang, T.
History
DepositionOct 17, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: YfiR
B: YfiB
C: YfiR
D: YfiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6996
Polymers64,5074
Non-polymers1922
Water9,620534
1
A: YfiR
B: YfiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3493
Polymers32,2532
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-34 kcal/mol
Surface area12820 Å2
MethodPISA
2
C: YfiR
D: YfiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3493
Polymers32,2532
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-35 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.499, 58.574, 69.863
Angle α, β, γ (deg.)72.930, 96.980, 90.190
Int Tables number1
Space group name H-MP1

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Components

#1: Protein YfiR


Mass: 17392.783 Da / Num. of mol.: 2 / Fragment: UNP residues 35-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: yfiR, PA1121 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q9I4L4
#2: Protein YfiB


Mass: 14860.617 Da / Num. of mol.: 2 / Fragment: UNP residues 34-168 / Mutation: L43P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: yfiB, PA1119 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q9I4L6
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 3.2 Å3/Da / Density % sol: 61.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M ammonium sulfate, 0.1 M Tris-HCl, 12%(w/v) polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 67774 / % possible obs: 96.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.036 / Rrim(I) all: 0.066 / Χ2: 0.712 / Net I/av σ(I): 17.75 / Net I/σ(I): 6.9 / Num. measured all: 224013
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.863.30.46366150.8490.2960.5510.55894.6
1.86-1.943.20.38467080.8320.2520.4620.84595.1
1.94-2.033.20.2467290.9330.1580.2890.62395.8
2.03-2.133.20.18967580.9160.1260.2280.75596.1
2.13-2.273.50.13868090.9670.0870.1640.81196.5
2.27-2.443.40.09167180.9880.0570.1080.6596.9
2.44-2.693.20.07268500.9870.0470.0860.66397.3
2.69-3.083.20.05268700.9940.0340.0620.67297.7
3.08-3.883.50.04369270.9960.0270.050.81198.3
3.88-503.30.03667900.9960.0230.0430.71597.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
d*TREKdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NY7, 5EAZ

4ny7

5eaz


Resolution: 1.8→37.623 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 22.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2061 3373 4.98 %Random selection
Rwork0.179 64344 --
obs0.1803 67717 95.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.58 Å2 / Biso mean: 35.345 Å2 / Biso min: 14.54 Å2
Refinement stepCycle: final / Resolution: 1.8→37.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4203 0 10 534 4747
Biso mean--45.51 43.51 -
Num. residues----543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074331
X-RAY DIFFRACTIONf_angle_d1.115853
X-RAY DIFFRACTIONf_chiral_restr0.047647
X-RAY DIFFRACTIONf_plane_restr0.005788
X-RAY DIFFRACTIONf_dihedral_angle_d12.9461651
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7808-1.80620.2976810.25311714179561
1.8062-1.83320.27671450.26872729287495
1.8332-1.86180.28821460.252617276395
1.8618-1.89240.26381350.2452711284695
1.8924-1.9250.3021530.25562656280994
1.925-1.960.2411390.22142711285096
1.96-1.99770.21371560.20122666282296
1.9977-2.03850.19781440.19962707285196
2.0385-2.08280.25111440.21472704284895
2.0828-2.13120.21741440.19752728287296
2.1312-2.18450.22021260.1912715284197
2.1845-2.24360.25471380.1942733287196
2.2436-2.30960.25651410.20582701284296
2.3096-2.38410.22171380.18692731286997
2.3841-2.46930.21351430.18742778292197
2.4693-2.56820.2281530.19052730288398
2.5682-2.6850.22861330.1942730286397
2.685-2.82650.1931270.18762765289297
2.8265-3.00360.23731410.19452759290098
3.0036-3.23530.21071530.17852754290798
3.2353-3.56070.21590.16112781294098
3.5607-4.07540.16931460.14862791293799
4.0754-5.13250.14491510.13592752290398
5.1325-37.63090.20261370.17082681281895

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