[English] 日本語
Yorodumi
- PDB-6kko: The crystal structure of SiaB-SiaC complex from Pseudomonas aeruginosa -

+
Open data


ID or keywords:

Loading...

-
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 / nucleotide binding / signal transduction
Similarity search - Function
Protein of unknown function DUF6272 / Family of unknown function (DUF6272) / 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 / Biofilm formation regulator SiaD modulator protein SiaC / Putative serine phosphatase / ATP-binding protein / SiaC family regulatory phosphoprotein 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
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUTHRTHR(chain A and (resseq 6:14 or resseq 16:20 or resseq...AA6 - 147 - 15
121GLNGLNLEULEU(chain A and (resseq 6:14 or resseq 16:20 or resseq...AA16 - 2017 - 21
131PHEPHESERSER(chain A and (resseq 6:14 or resseq 16:20 or resseq...AA22 - 2723 - 28
141SERSERMSEMSE(chain A and (resseq 6:14 or resseq 16:20 or resseq...AA29 - 5330 - 54
151GLUGLUILEILE(chain A and (resseq 6:14 or resseq 16:20 or resseq...AA2 - 1803 - 181
161GLUGLUILEILE(chain A and (resseq 6:14 or resseq 16:20 or resseq...AA2 - 1803 - 181
171GLUGLUILEILE(chain A and (resseq 6:14 or resseq 16:20 or resseq...AA2 - 1803 - 181
181GLUGLUILEILE(chain A and (resseq 6:14 or resseq 16:20 or resseq...AA2 - 1803 - 181
191GLUGLUILEILE(chain A and (resseq 6:14 or resseq 16:20 or resseq...AA2 - 1803 - 181
1101GLUGLUILEILE(chain A and (resseq 6:14 or resseq 16:20 or resseq...AA2 - 1803 - 181
1111GLUGLUILEILE(chain A and (resseq 6:14 or resseq 16:20 or resseq...AA2 - 1803 - 181
211LEULEUTHRTHR(chain B and (resseq 6:14 or resseq 16:20 or resseq...BB6 - 147 - 15
221GLNGLNLEULEU(chain B and (resseq 6:14 or resseq 16:20 or resseq...BB16 - 2017 - 21
231PHEPHESERSER(chain B and (resseq 6:14 or resseq 16:20 or resseq...BB22 - 2723 - 28
241SERSERILEILE(chain B and (resseq 6:14 or resseq 16:20 or resseq...BB0 - 1801 - 181
251SERSERILEILE(chain B and (resseq 6:14 or resseq 16:20 or resseq...BB0 - 1801 - 181
261SERSERILEILE(chain B and (resseq 6:14 or resseq 16:20 or resseq...BB0 - 1801 - 181
271SERSERILEILE(chain B and (resseq 6:14 or resseq 16:20 or resseq...BB0 - 1801 - 181
281SERSERILEILE(chain B and (resseq 6:14 or resseq 16:20 or resseq...BB0 - 1801 - 181
112SERSERSERSER(chain C and (resseq 0:25 or resseq 27:33 or (resid...CC0 - 251 - 26
122GLNGLNGLUGLU(chain C and (resseq 0:25 or resseq 27:33 or (resid...CC27 - 3328 - 34
132SERSERSERSER(chain C and (resseq 0:25 or resseq 27:33 or (resid...CC01
142SERSERGLUGLU(chain C and (resseq 0:25 or resseq 27:33 or (resid...CC0 - 1261 - 127
152SERSERGLUGLU(chain C and (resseq 0:25 or resseq 27:33 or (resid...CC0 - 1261 - 127
162SERSERGLUGLU(chain C and (resseq 0:25 or resseq 27:33 or (resid...CC0 - 1261 - 127
172SERSERGLUGLU(chain C and (resseq 0:25 or resseq 27:33 or (resid...CC0 - 1261 - 127
212SERSERSERSER(chain D and (resseq 0:25 or resseq 27:51 or resseq...DD0 - 251 - 26
222GLNGLNALAALA(chain D and (resseq 0:25 or resseq 27:51 or resseq...DD27 - 5128 - 52
232GLYGLYGLYGLY(chain D and (resseq 0:25 or resseq 27:51 or resseq...DD5354
242GLNGLNGLNGLN(chain D and (resseq 0:25 or resseq 27:51 or resseq...DD5455
252SERSERASPASP(chain D and (resseq 0:25 or resseq 27:51 or resseq...DD0 - 1251 - 126
262SERSERASPASP(chain D and (resseq 0:25 or resseq 27:51 or resseq...DD0 - 1251 - 126
272SERSERASPASP(chain D and (resseq 0:25 or resseq 27:51 or resseq...DD0 - 1251 - 126
282SERSERASPASP(chain D and (resseq 0:25 or resseq 27:51 or resseq...DD0 - 1251 - 126

NCS ensembles :
ID
1
2

-
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


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


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more