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- PDB-5eb0: crystal form II of YfiB belonging to P41 -

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Basic information

Entry
Database: PDB / ID: 5eb0
Titlecrystal form II of YfiB belonging to P41
ComponentsYfiB
KeywordsMEMBRANE PROTEIN / OmpA/Pal-like outer-membrane lipoprotein
Function / homology
Function and homology information


bacterial-type flagellum stator complex / bacterial-type flagellum-dependent cell motility / cell outer membrane
Similarity search - Function
OmpA-like domain / Outer membrane protein, bacterial / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / 60s Ribosomal Protein L30; Chain: A; / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Outer-membrane lipoprotein YfiB
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YfiB
B: YfiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8493
Polymers29,7532
Non-polymers961
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-4 kcal/mol
Surface area14200 Å2
Unit cell
Length a, b, c (Å)46.953, 46.953, 154.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein YfiB


Mass: 14876.660 Da / Num. of mol.: 2 / Fragment: UNP residues 34-168
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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.86 Å3/Da / Density % sol: 56.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M lithium sulfate monohydrate, 0.1 M Tris-HCl, 30%(w/v) polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 8105 / % possible obs: 97.8 % / Redundancy: 11.1 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.146 / Χ2: 0.929 / Net I/av σ(I): 12.5 / Net I/σ(I): 8.5 / Num. measured all: 89623
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.8511.50.4974120.556100
2.85-2.911.50.4544240.604100
2.9-2.9611.40.414040.633100
2.96-3.0211.60.3334100.69100
3.02-3.0811.60.3074080.737100
3.08-3.1511.50.2874250.828100
3.15-3.2311.50.2583950.86799.7
3.23-3.3211.60.2554261.019100
3.32-3.4211.40.2264041.018100
3.42-3.5311.30.2564191.84199.5
3.53-3.6511.30.1934141.13100
3.65-3.811.10.1963981.43100
3.8-3.9710.40.1814031.40897.1
3.97-4.1810.80.1564101.00598.3
4.18-4.4410.60.1463980.95596.8
4.44-4.7910.40.1363910.83992.2
4.79-5.2710.40.133960.81496.4
5.27-6.0310.80.1234090.74897.8
6.03-7.5910.40.1023960.57195.9
7.59-509.90.1013630.88683.6

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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: 3khn

3khn


Resolution: 2.8→46.953 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 24.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2649 369 4.61 %Random selection
Rwork0.1917 7640 --
obs0.195 8009 97.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.28 Å2 / Biso mean: 42.5976 Å2 / Biso min: 11.34 Å2
Refinement stepCycle: final / Resolution: 2.8→46.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 5 52 2143
Biso mean--66.52 36.09 -
Num. residues----270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092114
X-RAY DIFFRACTIONf_angle_d1.1322844
X-RAY DIFFRACTIONf_chiral_restr0.069310
X-RAY DIFFRACTIONf_plane_restr0.004386
X-RAY DIFFRACTIONf_dihedral_angle_d14.117810
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7983-3.20310.29231220.209426062728100
3.2031-4.03530.29981370.18532584272199
4.0353-46.95960.21841100.1882450256093

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