[English] 日本語
Yorodumi
- PDB-3w2z: Crystal structure of the cyanobacterial protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3w2z
TitleCrystal structure of the cyanobacterial protein
ComponentsMethyl-accepting chemotaxis proteinMethyl-accepting chemotaxis proteins
KeywordsSIGNALING PROTEIN / PHOTORECEPTOR / CYANOBACTERIOCHROME / GAF DOMAIN
Function / homology
Function and homology information


chemotaxis / transmembrane signaling receptor activity / signal transduction / membrane
Similarity search - Function
Chemotaxis methyl-accepting receptor / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / GAF domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. ...Chemotaxis methyl-accepting receptor / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / GAF domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHYCOCYANOBILIN / IODIDE ION / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesNostoc (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsNarikawa, R. / Muraki, N. / Shiba, T. / Kurisu, G. / Ikeuchi, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structures of cyanobacteriochromes from phototaxis regulators AnPixJ and TePixJ reveal general and specific photoconversion mechanism
Authors: Narikawa, R. / Ishizuka, T. / Muraki, N. / Shiba, T. / Kurisu, G. / Ikeuchi, M.
History
DepositionDec 6, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4983
Polymers22,7831
Non-polymers7162
Water3,333185
1
A: Methyl-accepting chemotaxis protein
hetero molecules

A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9976
Polymers45,5652
Non-polymers1,4314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5630 Å2
ΔGint-51 kcal/mol
Surface area16540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.133, 69.133, 124.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis proteins


Mass: 22782.717 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 221-397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc (bacteria) / Strain: PCC 7120 / Gene: all1069 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) PKT271 / References: UniProt: Q8YXY7
#2: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H40N4O6
#3: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 3.25 Å3/Da / Density % sol: 62.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 20% PEG8000, 0.2M POTASSIUM IODIDE, pH 7.5, VAPOR DIFFUSION, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2007
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 28763 / % possible obs: 99.7 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.057
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.399 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→28.31 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.395 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1448 5.1 %RANDOM
Rwork0.197 ---
obs0.199 27175 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.32 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1438 0 44 185 1667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221557
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9522121
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5675185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.62224.26775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69315257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.183158
X-RAY DIFFRACTIONr_chiral_restr0.1210.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021206
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2734
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21076
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5030.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.011.5909
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81221465
X-RAY DIFFRACTIONr_scbond_it2.63734
X-RAY DIFFRACTIONr_scangle_it4.3144.5656
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 96 -
Rwork0.272 1925 -
obs--97.96 %

+
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