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- PDB-6k4f: SiaC of Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6k4f
TitleSiaC of Pseudomonas aeruginosa
ComponentsDUF1987 domain-containing protein
KeywordsBIOSYNTHETIC PROTEIN / SiaC / Biofilm
Function / homologySiaC family regulatory phosphoprotein / SiaC family regulatory phosphoprotein / Biofilm formation regulator SiaD modulator protein SiaC / Uncharacterized protein PA14_02130
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.735 Å
AuthorsLin, J.Q. / Lescar, J.
CitationJournal: Plos One / Year: 2020
Title: The SiaABC threonine phosphorylation pathway controls biofilm formation in response to carbon availability in Pseudomonas aeruginosa.
Authors: Poh, W.H. / Lin, J. / Colley, B. / Muller, N. / Goh, B.C. / Schleheck, D. / El Sahili, A. / Marquardt, A. / Liang, Y. / Kjelleberg, S. / Lescar, J. / Rice, S.A. / Klebensberger, J.
History
DepositionMay 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Nov 3, 2021Group: Database references / Structure summary / Category: audit_author / database_2
Item: _audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
U: DUF1987 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)14,7861
Polymers14,7861
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.400, 72.800, 95.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11U-227-

HOH

21U-252-

HOH

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Components

#1: Protein DUF1987 domain-containing protein


Mass: 14786.435 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: ALP65_03379, CGU42_29970, DT376_26170, DY979_27175, DZ962_26905, EB236_19545, ECC04_17625, EFK27_14525, EFK68_31140, EGJ96_17530, EQH76_15975, IPC24_23845, IPC3_18980, PA34_000955, PAMH19_0166
Production host: Escherichia coli (E. coli) / References: UniProt: A0A072ZHB4, UniProt: Q02UQ8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.94 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M phosphate/citrate, PH4.2, 40% (v/v) PEG 300

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.735→57.96 Å / Num. obs: 13113 / % possible obs: 98.94 % / Redundancy: 8.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09846 / Rpim(I) all: 0.03468 / Net I/σ(I): 12.05
Reflection shellResolution: 1.735→1.797 Å / Rmerge(I) obs: 1.129 / Num. unique obs: 1176 / CC1/2: 0.62 / Rpim(I) all: 0.4561

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Processing

Software
NameVersionClassification
PHENIX(dev_3386: ???)refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.735→57.96 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.44
RfactorNum. reflection% reflection
Rfree0.2348 1228 5.03 %
Rwork0.1972 --
obs0.1991 13099 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.735→57.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 0 54 1025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008993
X-RAY DIFFRACTIONf_angle_d0.8841345
X-RAY DIFFRACTIONf_dihedral_angle_d7.986592
X-RAY DIFFRACTIONf_chiral_restr0.049141
X-RAY DIFFRACTIONf_plane_restr0.005179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7351-1.80450.41831200.39262274X-RAY DIFFRACTION87
1.8045-1.88670.33981370.33482627X-RAY DIFFRACTION100
1.8867-1.98620.35591400.30812587X-RAY DIFFRACTION100
1.9862-2.11060.23971430.22362613X-RAY DIFFRACTION100
2.1106-2.27360.22781350.20322601X-RAY DIFFRACTION100
2.2736-2.50240.22471430.19922658X-RAY DIFFRACTION100
2.5024-2.86450.24991380.1942592X-RAY DIFFRACTION100
2.8645-3.60880.23261350.18012599X-RAY DIFFRACTION100
3.6088-57.99530.20461370.17182628X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 14.7126 Å / Origin y: 16.1319 Å / Origin z: 14.027 Å
111213212223313233
T0.2629 Å2-0.0122 Å20.0155 Å2-0.2613 Å2-0.0062 Å2--0.2538 Å2
L1.6725 °2-0.3333 °2-1.105 °2-0.6598 °20.5282 °2--1.0749 °2
S0.1875 Å °-0.3218 Å °-0.0412 Å °-0.0853 Å °0.009 Å °0.0164 Å °-0.1782 Å °0.0611 Å °-0.0049 Å °
Refinement TLS groupSelection details: all

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