[English] 日本語
Yorodumi
- PDB-3olo: Crystal structure of a PAS domain from two-component sensor histi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3olo
TitleCrystal structure of a PAS domain from two-component sensor histidine kinase
ComponentsTwo-component sensor histidine kinase
KeywordsTRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / histidine kinase
Function / homology
Function and homology information


phosphorelay sensor kinase activity
Similarity search - Function
PAS domain / PAS domain / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal ...PAS domain / PAS domain / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Two-component sensor histidine kinase
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.094 Å
AuthorsMichalska, K. / Chhor, G. / Bearden, J. / Fenske, R.J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a PAS domain from two-component sensor histidine kinase
Authors: Michalska, K. / Chhor, G. / Bearden, J. / Fenske, R.J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionAug 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Two-component sensor histidine kinase
B: Two-component sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9434
Polymers28,7592
Non-polymers1842
Water95553
1
A: Two-component sensor histidine kinase
hetero molecules

A: Two-component sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9434
Polymers28,7592
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2470 Å2
ΔGint-30 kcal/mol
Surface area11320 Å2
MethodPISA
2
B: Two-component sensor histidine kinase
hetero molecules

B: Two-component sensor histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9434
Polymers28,7592
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
Buried area3200 Å2
ΔGint-29 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.43, 85.43, 67.84
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Two-component sensor histidine kinase


Mass: 14379.462 Da / Num. of mol.: 2 / Fragment: PAS domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr0428 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: Q8YZM9, histidine kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.05 M citric acid, 0.05 M BIS-TRIS propane, 16% (w/v) PEG3350, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 30, 2010 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.094→35 Å / Num. all: 15323 / Num. obs: 15260 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 16.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 2.4 / Num. unique all: 749 / % possible all: 100

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.094→30.202 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 881 5.79 %random
Rwork0.1772 ---
all0.1799 15213 --
obs0.1799 15213 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.704 Å2 / ksol: 0.424 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.9105 Å20 Å2-0 Å2
2--5.9105 Å20 Å2
3----11.8211 Å2
Refinement stepCycle: LAST / Resolution: 2.094→30.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 12 53 1950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071959
X-RAY DIFFRACTIONf_angle_d12634
X-RAY DIFFRACTIONf_dihedral_angle_d16.357728
X-RAY DIFFRACTIONf_chiral_restr0.067271
X-RAY DIFFRACTIONf_plane_restr0.003344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0942-2.22530.27111640.22372296X-RAY DIFFRACTION99
2.2253-2.39710.26141530.20552337X-RAY DIFFRACTION100
2.3971-2.63820.24391460.18962368X-RAY DIFFRACTION100
2.6382-3.01960.22961470.18042385X-RAY DIFFRACTION100
3.0196-3.80320.22241210.1552435X-RAY DIFFRACTION100
3.8032-30.20540.20341500.16932511X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9263-1.74181.56871.69050.9137.249-0.3959-0.05361.4370.48440.28242.0261-0.5854-1.1594-0.19990.4669-0.00290.1510.4931-0.02590.732953.619236.285720.1468
20.77450.8798-0.16822.06461.52723.047-0.04380.09060.006-0.15360.01590.1459-0.0466-0.1466-0.0030.25280.0157-0.01750.25050.04610.261355.48619.97765.3244
39.85575.3355.39614.3972.37873.16590.63390.189-0.00760.55830.0755-0.1335-0.4475-1.0952-0.03130.6507-0.0820.04510.63650.0540.578646.79166.691114.4851
40.3106-0.0631-0.50581.4435-0.62153.3104-0.16-0.1302-0.1302-0.03460.2270.01960.8128-0.2320.05650.3509-0.0744-0.03330.27070.03360.210954.683513.58047.8448
55.3739-3.5558-6.9958.42782.74659.97470.2909-0.93120.81760.6990.2352-0.8345-0.90540.7584-0.28980.2607-0.0861-0.06080.33550.05860.247760.565314.362811.2961
63.04643.08461.35253.27921.91082.62740.20220.6751-0.6223-0.5230.134-1.02690.36621.9837-1.32230.21230.07570.04340.5136-0.02760.358668.595722.554652.1667
72.57960.38230.34710.13880.52841.55590.0139-0.1662-0.19880.07390.0298-0.0436-0.0289-0.0848-0.00640.2-0.0020.00550.2050.03430.208950.421718.283451.594
82.47851.4823-1.16883.1913-1.52881.9595-0.05140.6222-0.0587-0.31940.1760.0593-0.0706-0.0730.04710.3401-0.05630.00230.4596-0.01760.252242.075218.160336.8427
93.51111.4604-0.92982.8811-3.29583.9702-0.0427-0.10080.09230.1945-0.0430.1095-0.13670.0070.0640.18110.035-0.03020.24650.02370.230338.010421.946447.8752
109.0464-3.1814-5.11834.09112.53263.98180.30630.070.3821-0.12850.0133-0.2429-0.19070.0681-0.12160.2395-0.026-0.02890.20950.01410.148653.239521.607241.0488
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:11)
2X-RAY DIFFRACTION2(chain A and resid 12:66)
3X-RAY DIFFRACTION3(chain A and resid 67:75)
4X-RAY DIFFRACTION4(chain A and resid 76:106)
5X-RAY DIFFRACTION5(chain A and resid 107:114)
6X-RAY DIFFRACTION6(chain B and resid 5:12)
7X-RAY DIFFRACTION7(chain B and resid 13:55)
8X-RAY DIFFRACTION8(chain B and resid 56:75)
9X-RAY DIFFRACTION9(chain B and resid 76:94)
10X-RAY DIFFRACTION10(chain B and resid 95:114)

+
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://pdbjlvh1.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