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- PDB-6kkp: The crystal structure of apo-SiaC from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6kkp
TitleThe crystal structure of apo-SiaC from Pseudomonas aeruginosa
ComponentsDUF1987 domain-containing protein
KeywordsGENE REGULATION / Pseudomonas aeruginosa / apo-SiaC / regulation
Function / homologySiaC family regulatory phosphoprotein / SiaC family regulatory phosphoprotein / Biofilm formation regulator SiaD modulator protein SiaC / SiaC family regulatory phosphoprotein domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGan, J.H. / Yang, C. / Chen, G.K. / Liang, H.H.
CitationJournal: Embo J. / Year: 2020
Title: The SiaA/B/C/D signaling network regulates biofilm formation in Pseudomonas aeruginosa.
Authors: Chen, G.K. / Gan, J.H. / Yang, C. / Zuo, Y.L. / Peng, J. / Li, M. / Huo, W.P. / Xie, Y.P. / Zhang, Y.N. / Wang, T.T. / Deng, X. / Liang, H.H.
History
DepositionJul 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF1987 domain-containing protein


Theoretical massNumber of molelcules
Total (without water)14,6551
Polymers14,6551
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6520 Å2
Unit cell
Length a, b, c (Å)35.627, 72.057, 96.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein DUF1987 domain-containing protein / SiaC


Mass: 14655.237 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A072ZHB4, UniProt: Q9I6W2*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.4M NaH2PO4/1.6M K2HPO4, 0.1M imidazole PH 8.0, 0.2M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 4479 / % possible obs: 98.5 % / Redundancy: 6.4 % / CC1/2: 0.971 / Net I/σ(I): 15.4
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 4.5 / Num. unique obs: 415 / CC1/2: 0.939

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KKO

6kko


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.906 / SU B: 10.034 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.967 / ESU R Free: 0.311
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2514 200 4.5 %RANDOM
Rwork0.209 ---
obs0.2108 4208 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 64.91 Å2 / Biso mean: 31.902 Å2 / Biso min: 14.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0 Å2
2--0.11 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 0 11 977
Biso mean---26.22 -
Num. residues----121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.019988
X-RAY DIFFRACTIONr_bond_other_d0.0010.02903
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.9541339
X-RAY DIFFRACTIONr_angle_other_deg0.88432069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4565119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05123.77453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62515159
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.911159
X-RAY DIFFRACTIONr_chiral_restr0.0650.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211135
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02240
LS refinement shellResolution: 2.5→2.564 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 13 -
Rwork0.244 257 -
all-270 -
obs--85.99 %

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