[English] 日本語
- PDB-2p04: 2.1 Ang structure of the dimerized PAS domain of signal transduct... -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 2p04
Title2.1 Ang structure of the dimerized PAS domain of signal transduction histidine kinase from Nostoc punctiforme PCC 73102 with homology to the H-NOXA/H-NOBA domain of the soluble guanylyl cyclase
Componentssignal transduction histidine kinaseTwo-component regulatory system
KeywordsTRANSFERASE / PAS-like fold dimer / homologous to soluble guanylyl cyclase domain
Function / homology
Function and homology information

guanylate cyclase / guanylate cyclase activity / nucleotide binding
Similarity search - Function
Haem NO binding associated domain / Haem NO binding associated domain superfamily / Haem NO binding associated / Heme NO binding associated / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesNostoc punctiforme (Cyanobacteria)
Authorsvan den Akker, F. / Ma, X.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: PAS-mediated dimerization of soluble guanylyl cyclase revealed by signal transduction histidine kinase domain crystal structure.
Authors: Ma, X. / Sayed, N. / Baskaran, P. / Beuve, A. / van den Akker, F.
DepositionFeb 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance

Structure visualization

Structure viewerMolecule:

Downloads & links


Deposited unit
A: signal transduction histidine kinase
B: signal transduction histidine kinase

Theoretical massNumber of molelcules
Total (without water)27,7402

  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-17 kcal/mol
Surface area10870 Å2
Unit cell
Length a, b, c (Å)95.210, 44.362, 59.740
Angle α, β, γ (deg.)90.00, 104.51, 90.00
Int Tables number5
Space group name H-MC121


#1: Protein signal transduction histidine kinase / Two-component regulatory system

Mass: 13870.230 Da / Num. of mol.: 2 / Fragment: H-NOXA/H-NOBA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (Cyanobacteria) / Strain: PCC 73102 / Gene: COG0642 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: D0VWX5*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O

Experimental details


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

Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes pH 7.5, 1.5M LiSO4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 12364 / % possible obs: 87.4 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.119 / Net I/σ(I): 10
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.456 / % possible all: 59.8


HKL-3000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Truncated delta-7 H-NOXA structure

Resolution: 2.11→25.26 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.062 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.262 614 5 %RANDOM
Rwork0.19928 ---
obs0.20232 11666 86.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.334 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.11→25.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 0 55 1787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221782
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9782410
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.485210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.1452485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.05115315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5591510
X-RAY DIFFRACTIONr_chiral_restr0.0980.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021360
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2780
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21219
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.592.51110
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.913.51739
X-RAY DIFFRACTIONr_scbond_it4.743751
X-RAY DIFFRACTIONr_scangle_it6.6444.5671
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 2.11 Å / Num. reflection Rwork: 556 / Total num. of bins used: 20

About Yorodumi


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


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