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- PDB-4yn9: YfiR mutant-C110S -

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Basic information

Entry
Database: PDB / ID: 4yn9
TitleYfiR mutant-C110S
ComponentsYfiR
KeywordsTRANSCRIPTION / Periplasmic Repressor Protein / C110S mutant
Function / homologyYfiR/HmsC-like / YfiR/HmsC-like / periplasmic space / Negative regulator YfiR
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsXu, M. / Jiang, T.
Funding support China, 1items
OrganizationGrant numberCountry
the Strategic Priority Research ProgramXDB08010301 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structures of YfiR from Pseudomonas aeruginosa in two redox states
Authors: Yang, X. / Yang, X.-A. / Xu, M. / Zhou, L. / Fan, Z. / Jiang, T.
History
DepositionMar 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YfiR
B: YfiR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9464
Polymers34,7532
Non-polymers1922
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-45 kcal/mol
Surface area14660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.011, 121.011, 86.513
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein YfiR


Mass: 17376.719 Da / Num. of mol.: 2 / Fragment: UNP residues 35-190 / Mutation: C110S
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: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.71 Å3/Da / Density % sol: 73.88 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 1.8 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 23583 / % possible obs: 97.3 % / Redundancy: 10.6 % / Biso Wilson estimate: 30.21 Å2 / Rmerge(I) obs: 0.069 / Χ2: 1.039 / Net I/av σ(I): 27.865 / Net I/σ(I): 13.4 / Num. measured all: 249982
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.45-2.4910.70.38111580.96398
2.49-2.5410.70.34911700.93998.5
2.54-2.5910.70.311690.93899.2
2.59-2.6410.70.27811710.93298.1
2.64-2.710.80.24311780.95398.7
2.7-2.7610.70.18911820.92799.2
2.76-2.8310.80.15811520.92998
2.83-2.910.80.14411790.89298
2.9-2.9910.80.12511740.9198
2.99-3.0910.80.09611850.91398.4
3.09-3.210.70.08111640.86598.1
3.2-3.3210.70.0711690.90197.7
3.32-3.4810.70.06811891.04797.8
3.48-3.6610.70.0711811.17898.1
3.66-3.8910.70.07811811.67397.4
3.89-4.1910.60.07911811.84897.1
4.19-4.6110.40.0711801.70396.2
4.61-5.2810.30.05111980.8496.3
5.28-6.6510.40.03411930.38694.8
6.65-509.40.02912291.05690.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YN7

4yn7


Resolution: 2.45→38.604 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 1057 5.11 %0
Rwork0.1885 19636 --
obs0.1908 20693 85.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.24 Å2 / Biso mean: 37.0578 Å2 / Biso min: 7.28 Å2
Refinement stepCycle: final / Resolution: 2.45→38.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 0 148 2467
Biso mean---37.79 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082366
X-RAY DIFFRACTIONf_angle_d1.0353203
X-RAY DIFFRACTIONf_chiral_restr0.041366
X-RAY DIFFRACTIONf_plane_restr0.005422
X-RAY DIFFRACTIONf_dihedral_angle_d14.863889
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4503-2.56180.2452970.19461794189164
2.5618-2.69680.26561090.19862012212172
2.6968-2.86580.2661290.2062225235479
2.8658-3.08690.25211340.21222495262988
3.0869-3.39740.25761330.20082654278794
3.3974-3.88860.20371620.15892790295297
3.8886-4.89770.17381480.15582800294897
4.8977-38.60890.28491450.21812866301193
Refinement TLS params.Method: refined / Origin x: 35.9687 Å / Origin y: -14.842 Å / Origin z: -24.9913 Å
111213212223313233
T0.104 Å20.0161 Å2-0.0421 Å2-0.0893 Å2-0.013 Å2--0.0705 Å2
L0.5832 °20.3482 °2-0.073 °2-0.6757 °20.3414 °2--0.6264 °2
S-0.0554 Å °0.0393 Å °0.0748 Å °-0.0737 Å °-0.0285 Å °0.0279 Å °-0.1516 Å °0.0656 Å °-0.0266 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA38 - 190
2X-RAY DIFFRACTION1allB38 - 185
3X-RAY DIFFRACTION1allA201
4X-RAY DIFFRACTION1allB201
5X-RAY DIFFRACTION1allA301 - 390
6X-RAY DIFFRACTION1allB301 - 358

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