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- PDB-8ju9: Molecular mechanism of the one-component regulator RccR on bacter... -

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Basic information

Entry
Database: PDB / ID: 8ju9
TitleMolecular mechanism of the one-component regulator RccR on bacterial metabolism and virulence
ComponentsProbable transcriptional regulator
KeywordsDNA BINDING PROTEIN / One-component systems / KDPG-binding
Function / homology2-KETO-DEOXY-GALACTOSE / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRui, B. / Yibo, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)81871615 China
Citation
Journal: Nucleic Acids Res. / Year: 2024
Title: Molecular mechanism of the one-component regulator RccR on bacterial metabolism and virulence.
Authors: Zhu, Y. / Mou, X. / Song, Y. / Zhang, Q. / Sun, B. / Liu, H. / Tang, H. / Bao, R.
#1: Journal: To Be Published
Title: Molecular mechanism of the one-component regulator RccR on bacterial metabolism and virulence
Authors: Rui, B. / Yibo, Z.
History
DepositionJun 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8545
Polymers30,2061
Non-polymers6494
Water1,67593
1
A: Probable transcriptional regulator
hetero molecules

A: Probable transcriptional regulator
hetero molecules

A: Probable transcriptional regulator
hetero molecules

A: Probable transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,41720
Polymers120,8234
Non-polymers2,59416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
Buried area23410 Å2
ΔGint-81 kcal/mol
Surface area39640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.319, 82.855, 138.622
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-843-

HOH

21A-859-

HOH

31A-875-

HOH

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Components

#1: Protein Probable transcriptional regulator


Mass: 30205.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA5438 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-KDP / 2-KETO-DEOXY-GALACTOSE


Mass: 258.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.36 Å3/Da / Density % sol: 63.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris (pH 8.0), 8%PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→27.66 Å / Num. obs: 29112 / % possible obs: 98.97 % / Redundancy: 5.2 % / Biso Wilson estimate: 32.79 Å2 / CC1/2: 1 / Net I/σ(I): 25.28
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 2760 / CC1/2: 0.858

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000v1.0data reduction
HKL-2000v1.0data scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→27.66 Å / SU ML: 0.1856 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2898 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2003 1997 6.87 %
Rwork0.1751 27051 -
obs0.1765 29048 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.28 Å2
Refinement stepCycle: LAST / Resolution: 2→27.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2141 0 16 93 2250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012188
X-RAY DIFFRACTIONf_angle_d1.22072954
X-RAY DIFFRACTIONf_chiral_restr0.0575353
X-RAY DIFFRACTIONf_plane_restr0.0074376
X-RAY DIFFRACTIONf_dihedral_angle_d15.04771328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0710.31811330.2851804X-RAY DIFFRACTION93.64
2.05-2.110.24551360.24551846X-RAY DIFFRACTION96.26
2.11-2.170.25621420.21631932X-RAY DIFFRACTION99.23
2.17-2.240.25141420.1921918X-RAY DIFFRACTION100
2.24-2.320.25341410.17691917X-RAY DIFFRACTION99.71
2.32-2.410.2421440.17791946X-RAY DIFFRACTION99.81
2.41-2.520.19131410.17671913X-RAY DIFFRACTION99.81
2.52-2.650.22591430.17911920X-RAY DIFFRACTION99.47
2.65-2.820.23861440.18231942X-RAY DIFFRACTION99.95
2.82-3.040.24691420.19151937X-RAY DIFFRACTION99.86
3.04-3.340.21631450.19461950X-RAY DIFFRACTION99.81
3.34-3.820.18791450.17161973X-RAY DIFFRACTION99.95
3.82-4.810.15051460.13551983X-RAY DIFFRACTION100

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