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- PDB-6kko: The crystal structure of SiaB-SiaC complex from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6kko
TitleThe crystal structure of SiaB-SiaC complex from Pseudomonas aeruginosa
Components
  • DUF1987 domain-containing protein
  • Putative serine phosphatase
KeywordsGENE REGULATION / SiaB-SiaC complex / Pseudomonas aeruginosa
Function / homology
Function and homology information


phosphatase activity / membrane => GO:0016020 / signal transduction
Similarity search - Function
SiaC family regulatory phosphoprotein / SiaC family regulatory phosphoprotein / Stage II sporulation protein E (SpoIIE) / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DUF1987 domain-containing protein / Putative serine phosphatase / Uncharacterized protein / SiaC domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.099 Å
AuthorsGan, J.H. / Yang, C.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative serine phosphatase
B: Putative serine phosphatase
C: DUF1987 domain-containing protein
D: DUF1987 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9508
Polymers70,0504
Non-polymers9004
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
ΔGint-88 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.618, 42.015, 96.584
Angle α, β, γ (deg.)90.000, 93.450, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 6:14 or resseq 16:20 or resseq...
21(chain B and (resseq 6:14 or resseq 16:20 or resseq...
12(chain C and (resseq 0:25 or resseq 27:33 or (resid...
22(chain D and (resseq 0:25 or resseq 27:51 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 6:14 or resseq 16:20 or resseq...A6 - 14
121(chain A and (resseq 6:14 or resseq 16:20 or resseq...A16 - 20
131(chain A and (resseq 6:14 or resseq 16:20 or resseq...A22 - 27
141(chain A and (resseq 6:14 or resseq 16:20 or resseq...A29 - 53
151(chain A and (resseq 6:14 or resseq 16:20 or resseq...A2 - 180
161(chain A and (resseq 6:14 or resseq 16:20 or resseq...A2 - 180
171(chain A and (resseq 6:14 or resseq 16:20 or resseq...A2 - 180
181(chain A and (resseq 6:14 or resseq 16:20 or resseq...A2 - 180
191(chain A and (resseq 6:14 or resseq 16:20 or resseq...A2 - 180
1101(chain A and (resseq 6:14 or resseq 16:20 or resseq...A2 - 180
1111(chain A and (resseq 6:14 or resseq 16:20 or resseq...A2 - 180
211(chain B and (resseq 6:14 or resseq 16:20 or resseq...B6 - 14
221(chain B and (resseq 6:14 or resseq 16:20 or resseq...B16 - 20
231(chain B and (resseq 6:14 or resseq 16:20 or resseq...B22 - 27
241(chain B and (resseq 6:14 or resseq 16:20 or resseq...B0 - 180
251(chain B and (resseq 6:14 or resseq 16:20 or resseq...B0 - 180
261(chain B and (resseq 6:14 or resseq 16:20 or resseq...B0 - 180
271(chain B and (resseq 6:14 or resseq 16:20 or resseq...B0 - 180
281(chain B and (resseq 6:14 or resseq 16:20 or resseq...B0 - 180
112(chain C and (resseq 0:25 or resseq 27:33 or (resid...C0 - 25
122(chain C and (resseq 0:25 or resseq 27:33 or (resid...C27 - 33
132(chain C and (resseq 0:25 or resseq 27:33 or (resid...C0
142(chain C and (resseq 0:25 or resseq 27:33 or (resid...C0 - 126
152(chain C and (resseq 0:25 or resseq 27:33 or (resid...C0 - 126
162(chain C and (resseq 0:25 or resseq 27:33 or (resid...C0 - 126
172(chain C and (resseq 0:25 or resseq 27:33 or (resid...C0 - 126
212(chain D and (resseq 0:25 or resseq 27:51 or resseq...D0 - 25
222(chain D and (resseq 0:25 or resseq 27:51 or resseq...D27 - 51
232(chain D and (resseq 0:25 or resseq 27:51 or resseq...D53
242(chain D and (resseq 0:25 or resseq 27:51 or resseq...D54
252(chain D and (resseq 0:25 or resseq 27:51 or resseq...D0 - 125
262(chain D and (resseq 0:25 or resseq 27:51 or resseq...D0 - 125
272(chain D and (resseq 0:25 or resseq 27:51 or resseq...D0 - 125
282(chain D and (resseq 0:25 or resseq 27:51 or resseq...D0 - 125

NCS ensembles :
ID
1
2

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Components

#1: Protein Putative serine phosphatase / SiaB


Mass: 20102.162 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A485GYA3, UniProt: Q9I6W1*PLUS
#2: Protein DUF1987 domain-containing protein / SiaC


Mass: 14922.800 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: the polypeptide is phosphorylated on thr (68) / Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A072ZHB4, UniProt: Q9I6W2*PLUS
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.27 Å3/Da / Density % sol: 45.91 % / Description: schistose
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris pH 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9725 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 2.099→37.74 Å / Num. obs: 35956 / % possible obs: 98.7 % / Redundancy: 3.3 % / CC1/2: 0.997 / Net I/σ(I): 9.4
Reflection shellResolution: 2.099→2.23 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2 / Num. unique obs: 10896 / CC1/2: 0.779 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.099→37.74 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2777 1646 4.61 %
Rwork0.2316 --
obs0.2338 35672 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.43 Å2 / Biso mean: 42.8974 Å2 / Biso min: 14.46 Å2
Refinement stepCycle: final / Resolution: 2.099→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 56 135 4821
Biso mean--62.8 41.38 -
Num. residues----591
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1284X-RAY DIFFRACTION7.414TORSIONAL
12B1284X-RAY DIFFRACTION7.414TORSIONAL
21C1114X-RAY DIFFRACTION7.414TORSIONAL
22D1114X-RAY DIFFRACTION7.414TORSIONAL
LS refinement shellResolution: 2.099→2.1608 Å
RfactorNum. reflection% reflection
Rfree0.3339 --
Rwork0.2954 --
obs-2695 97 %
Refinement TLS params.Method: refined / Origin x: 53.5396 Å / Origin y: 12.5397 Å / Origin z: 25.1139 Å
111213212223313233
T0.1918 Å2-0.0007 Å20.0018 Å2-0.135 Å20 Å2--0.175 Å2
L1.0205 °2-0.0062 °2-0.0001 °2-0.546 °20.0131 °2--0.4224 °2
S-0.0411 Å °0.113 Å °-0.0101 Å °-0.031 Å °0.0564 Å °-0.0329 Å °0.0042 Å °-0.0025 Å °-0.0203 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 180
2X-RAY DIFFRACTION1allB0 - 180
3X-RAY DIFFRACTION1allC0 - 126
4X-RAY DIFFRACTION1allD0 - 125
5X-RAY DIFFRACTION1allE1001 - 2101
6X-RAY DIFFRACTION1allS1 - 135

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