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- PDB-4yna: Oxidized YfiR -

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Basic information

Entry
Database: PDB / ID: 4yna
TitleOxidized YfiR
ComponentsYfiR
KeywordsTRANSCRIPTION / Periplasmic Repressor Protein / oxidized form
Function / homologyYfiR/HmsC-like / YfiR/HmsC-like / periplasmic space / Negative regulator YfiR
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 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 / Structure summary
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 / struct_keywords
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 / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YfiR
B: YfiR
C: YfiR
D: YfiR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7636
Polymers69,5714
Non-polymers1922
Water0
1
A: YfiR
B: YfiR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9784
Polymers34,7862
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-45 kcal/mol
Surface area14610 Å2
MethodPISA
2
C: YfiR
D: YfiR


Theoretical massNumber of molelcules
Total (without water)34,7862
Polymers34,7862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-5 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.668, 119.668, 85.776
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: 17392.783 Da / Num. of mol.: 4 / 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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 2.28 Å3/Da / Density % sol: 46.06 %
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: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54187 Å
DetectorType: RIGAKU / Detector: CCD / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 10704 / % possible obs: 98.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.164 / Χ2: 0.969 / Net I/av σ(I): 10.424 / Net I/σ(I): 5.1 / Num. measured all: 74115
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.2-3.2670.4865100.867100
3.26-3.3170.4635330.85699.6
3.31-3.3870.3975230.829100
3.38-3.4570.3495340.84299.6
3.45-3.527.10.3365310.91100
3.52-3.66.90.3075321.10199.6
3.6-3.6970.2535170.925100
3.69-3.7970.2175250.93799.2
3.79-3.9170.2275301.11599.8
3.91-4.037.10.1845300.92999.4
4.03-4.1870.1785241.06799.2
4.18-4.3470.1465420.93999.3
4.34-4.5470.1235351.05399.1
4.54-4.7870.1115330.90198.9
4.78-5.086.90.1265321.04498.9
5.08-5.4770.1335450.9698.9
5.47-6.026.90.1365380.97998.9
6.02-6.896.80.1265420.96197.8
6.89-8.676.70.0765631.05497.1
8.67-5060.0545851.13294.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YN7
Resolution: 3.2→34.88 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.836 / SU B: 20.337 / SU ML: 0.373 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.687 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2808 450 4.8 %RANDOM
Rwork0.2463 ---
obs0.2479 8904 86.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 249.82 Å2 / Biso mean: 94.62 Å2 / Biso min: 23.17 Å2
Baniso -1Baniso -2Baniso -3
1--2.18 Å2-0 Å2-0 Å2
2---2.18 Å20 Å2
3---4.36 Å2
Refinement stepCycle: final / Resolution: 3.2→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4584 0 10 0 4594
Biso mean--56.83 --
Num. residues----595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194673
X-RAY DIFFRACTIONr_bond_other_d0.0070.024594
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9666335
X-RAY DIFFRACTIONr_angle_other_deg0.8493.00310455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8025591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2121.963214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76115787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9561564
X-RAY DIFFRACTIONr_chiral_restr0.0640.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215330
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021118
LS refinement shellResolution: 3.196→3.279 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 28 -
Rwork0.238 433 -
all-461 -
obs--60.03 %

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