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- PDB-5y62: YfiR complexed with GMP -

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Basic information

Entry
Database: PDB / ID: 5y62
TitleYfiR complexed with GMP
ComponentsYfiR
KeywordsSIGNALING PROTEIN / YfiR / GMP / biofilm
Function / homologyYfiR/HmsC-like / YfiR/HmsC-like / periplasmic space / GUANOSINE-5'-MONOPHOSPHATE / Negative regulator YfiR
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhou, L. / Xu, M. / Jiang, T.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570768 China
Strategic Priority Research ProgramXDB08010301 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Structural insights into the functional role of GMP in modulating the YfiBNR system
Authors: Zhou, L. / Xu, M. / Jiang, T.
History
DepositionAug 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YfiR
B: YfiR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0353
Polymers34,6712
Non-polymers3631
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-2 kcal/mol
Surface area15100 Å2
Unit cell
Length a, b, c (Å)120.297, 120.297, 88.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein YfiR


Mass: 17335.732 Da / Num. of mol.: 2 / Fragment: UNP residues 35-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: yfiR, PA1121 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4L4
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
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: 4.74 Å3/Da / Density % sol: 74.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Hepes (pH 7.5), 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9779 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 3→49.73 Å / Num. obs: 13528 / % possible obs: 100 % / Redundancy: 25.1 % / Net I/σ(I): 22.12
Reflection shellResolution: 3→3.05 Å / Mean I/σ(I) obs: 5.2 / Num. unique obs: 667

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.8.2_1309phasing
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YN7

4yn7


Resolution: 3→49.727 Å / SU ML: 0.38 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 24.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2524 593 4.76 %
Rwork0.2011 --
obs0.2035 12454 92.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→49.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 24 0 2343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112386
X-RAY DIFFRACTIONf_angle_d1.263231
X-RAY DIFFRACTIONf_dihedral_angle_d15.549898
X-RAY DIFFRACTIONf_chiral_restr0.074370
X-RAY DIFFRACTIONf_plane_restr0.005423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0004-3.30220.32221300.24372295X-RAY DIFFRACTION74
3.3022-3.77990.22461530.19933001X-RAY DIFFRACTION95
3.7799-4.76170.24341630.17463184X-RAY DIFFRACTION100
4.7617-49.73420.25361470.21153381X-RAY DIFFRACTION100

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