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- PDB-5eaz: crystal form I of YfiB belonging to space groups P21 -

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Basic information

Entry
Database: PDB / ID: 5eaz
Titlecrystal form I of YfiB belonging to space groups P21
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 / MOLECULAR REPLACEMENT / Resolution: 2.151 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
C: YfiB
D: YfiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6035
Polymers59,5074
Non-polymers961
Water7,350408
1
A: YfiB
B: YfiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8493
Polymers29,7532
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: YfiB
D: YfiB


Theoretical massNumber of molelcules
Total (without water)29,7532
Polymers29,7532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.849, 90.449, 66.304
Angle α, β, γ (deg.)90.000, 113.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
YfiB


Mass: 14876.660 Da / Num. of mol.: 4 / 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.: 408 / 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: 3.03 Å3/Da / Density % sol: 59.46 %
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: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54187 Å
DetectorType: RIGAKU / Detector: CCD / Date: Jan 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 37635 / % possible obs: 97.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 19.78 Å2 / Rmerge(I) obs: 0.068 / Χ2: 0.928 / Net I/av σ(I): 19.257 / Net I/σ(I): 9.6 / Num. measured all: 159447
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.15-2.193.90.44718651.00895.3
2.19-2.2340.40517940.98495.4
2.23-2.2740.37318681.07294.6
2.27-2.3240.38518181.26295.6
2.32-2.3740.29618140.71994.1
2.37-2.424.10.24918190.65494.8
2.42-2.484.10.23318270.64694.3
2.48-2.554.10.20318320.68495
2.55-2.624.10.17318450.69496.2
2.62-2.714.10.15218700.7696.7
2.71-2.814.20.13118730.77497.2
2.81-2.924.20.11119090.82598.3
2.92-3.054.30.09419070.90699.1
3.05-3.214.40.07719440.94799.4
3.21-3.414.50.06519131.01199.7
3.41-3.684.50.05719451.06599.7
3.68-4.054.60.05219201.19599.7
4.05-4.634.60.04719591.17499.8
4.63-5.834.60.04519581.045100
5.83-504.40.03919550.98197.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
d*TREKdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3khn

3khn


Resolution: 2.151→23.128 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2629 1667 4.96 %Random selection
Rwork0.2014 31947 --
obs0.2045 33614 86.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.46 Å2 / Biso mean: 26.3534 Å2 / Biso min: 1.76 Å2
Refinement stepCycle: final / Resolution: 2.151→23.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4172 0 5 408 4585
Biso mean--37.16 32.91 -
Num. residues----540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094313
X-RAY DIFFRACTIONf_angle_d1.0855812
X-RAY DIFFRACTIONf_chiral_restr0.049628
X-RAY DIFFRACTIONf_plane_restr0.004797
X-RAY DIFFRACTIONf_dihedral_angle_d13.6321669
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1506-2.21380.2621520.20441112116436
2.2138-2.28520.2924950.21361807190260
2.2852-2.36680.31941080.23622290239875
2.3668-2.46150.31071570.23832656281387
2.4615-2.57340.31081510.24752843299494
2.5734-2.70880.30411570.24322927308496
2.7088-2.87830.34981480.24933007315597
2.8783-3.10.30761520.23513014316699
3.1-3.41110.28561620.194830413203100
3.4111-3.90260.22211480.173430783226100
3.9026-4.90920.21451780.159730383216100
4.9092-23.12940.20511590.181831343293100

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