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- PDB-5y61: YfiB-YfiR complexed with GMP -

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Basic information

Entry
Database: PDB / ID: 5y61
TitleYfiB-YfiR complexed with GMP
Components
  • YfiB
  • YfiR
KeywordsSIGNALING PROTEIN / YfiB-YfiR complex / GMP / biofilm
Function / homology
Function and homology information


cell outer membrane / periplasmic space
Similarity search - Function
YfiR/HmsC-like / YfiR/HmsC-like / OmpA-like domain / Outer membrane protein, bacterial / : / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / 60s Ribosomal Protein L30; Chain: A; ...YfiR/HmsC-like / YfiR/HmsC-like / OmpA-like domain / Outer membrane protein, bacterial / : / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / 60s Ribosomal Protein L30; Chain: A; / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / Negative regulator YfiR / Outer-membrane lipoprotein YfiB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 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 13, 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: YfiB
C: YfiR
D: YfiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3785
Polymers65,0154
Non-polymers3631
Water00
1
A: YfiR
B: YfiB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8713
Polymers32,5072
Non-polymers3631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-16 kcal/mol
Surface area13180 Å2
MethodPISA
2
C: YfiR
D: YfiB


Theoretical massNumber of molelcules
Total (without water)32,5072
Polymers32,5072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-16 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.595, 58.422, 69.869
Angle α, β, γ (deg.)107.39, 97.28, 89.90
Int Tables number1
Space group name H-MP1

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Components

#1: Protein YfiR


Mass: 17429.523 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: Protein YfiB


Mass: 15077.844 Da / Num. of mol.: 2 / Fragment: UNP residues 34-168
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: yfiB, PA1119 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4L6
#3: 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: 3.13 Å3/Da / Density % sol: 60.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl (pH 8.5) , 8% w/v polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.99→42.21 Å / Num. obs: 14631 / % possible obs: 97.8 % / Redundancy: 3.8 % / Net I/σ(I): 11.3
Reflection shellResolution: 3→3.05 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.33 / Num. unique obs: 746 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EB1

5eb1


Resolution: 2.99→42.207 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.96 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 688 5.02 %
Rwork0.1966 --
obs0.1997 13709 91.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.99→42.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4270 0 24 0 4294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094362
X-RAY DIFFRACTIONf_angle_d1.2425888
X-RAY DIFFRACTIONf_dihedral_angle_d16.1531661
X-RAY DIFFRACTIONf_chiral_restr0.075656
X-RAY DIFFRACTIONf_plane_restr0.004785
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9898-3.22060.31521130.24272096X-RAY DIFFRACTION73
3.2206-3.54450.31241280.23292602X-RAY DIFFRACTION91
3.5445-4.05710.28951680.21272731X-RAY DIFFRACTION97
4.0571-5.11010.22311340.16952818X-RAY DIFFRACTION98
5.1101-42.21110.22451450.18132774X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -52.7272 Å / Origin y: -20.7744 Å / Origin z: -28.6215 Å
111213212223313233
T0.1343 Å2-0.0072 Å20.0211 Å2-0.1315 Å20.018 Å2--0.1298 Å2
L0.3239 °20.074 °20.1714 °2-0.583 °20.2069 °2--0.3153 °2
S-0.0172 Å °0.0389 Å °-0.0065 Å °-0.0598 Å °0.0556 Å °-0.0465 Å °-0.0247 Å °0.0725 Å °-0.0198 Å °
Refinement TLS groupSelection details: all

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